QIAGEN IPA

From ‘Omics to Insights Part 2: Interpret Your IPA Core Analysis Results

Thu, 19 Mar 2026 21:35:59 GMT

This is the second part of a series on how you can easily turn your ‘omics data into actionable insights using QIAGEN Ingenuity Pathway Analysis (IPA). Here, we’ll introduce you to the QIAGEN Knowledge Base and the different sets of results you can get from an IPA Core Analysis.

You will learn:

How to predict the activity of enriched pathways, regulators, diseases and more
How to validate your results by comparing with published datasets
How to identify key biological themes in your data with the help of AI summaries

About this series

From ‘Omics to Insights: Data Analysis Fundamentals with IPA

Do you find ‘omics data analysis overwhelming? Good news: it doesn’t have to be.

Discover how you can easily turn your ‘omics data into actionable insights with QIAGEN Ingenuity Pathway Analysis (IPA), an advanced tertiary analysis program for your RNA-seq, proteomics or metabolomics dataset. Learn how to search the QIAGEN Knowledge Base, the rich, expert-curated content that powers IPA. Explore the biological landscape around a gene of interest, formulate promising hypotheses and uncover potentially novel connections – without worrying about programming or paywalls.

IPA Interpret: A hands-on workshop

Wed, 18 Mar 2026 08:58:36 GMT

Now, you can access and share the interpretative power of QIAGEN Ingenuity Pathway Analysis (IPA) in an easy-to-consume format – without installing any extra software. IPA Interpret identifies and summarizes the biological themes in your results with the help of AI, creating a shareable, interactive report.

You will learn how to:

- Create an IPA Interpret report that can be easily shared with others
- Gain valuable insight into critical biological pathways, key regulators and more with just a few clicks
- Easily customize charts, such as the highly popular volcano bubble chart, taking advantage of new features introduced with recent updates
- Export both graphical and tabular results

IPA deeper dive miRNA investigation using QIAGEN Ingenuity Pathway Analysis

Mon, 16 Mar 2026 11:17:11 GMT

In this 90-minute training session, you will learn how to identify target mRNAs for your miRNAs of interest and associate them with pathways, diseases, biological functions, tissues and cell types.

Topics that will be covered include:

How to analyze miRNA-seq datasets alone or both miRNA and corresponding mRNA datasets together
How to use QIAGEN IPA without a dataset, using miRNA IDs
Introduction to databases and curated content specific to miRNA
How to effectively apply various filters and functionalities to identify biomarkers, key targets and biological mechanisms

From ‘Omics to Insights Part 1: IPA Dataset Prep and Core Analysis Setup

Fri, 13 Mar 2026 11:16:05 GMT

This is the first part of a series on how you can easily turn your ‘omics data into actionable insights using QIAGEN Ingenuity Pathway Analysis (IPA). Here, we'll focus on setting up your dataset for IPA upload and analysis.

You will learn:

The IDs, measurement types and formats that IPA supports
How IPA uses your data for statistical tests and prediction scoring
The different types and parameters of a Core Analysis
Best practice tips from our expert

About this series

From ‘Omics to Insights: Data Analysis Fundamentals with IPA

Do you find ‘omics data analysis overwhelming? Good news: it doesn’t have to be.

Multi-omics (metabolomics, proteomics, transcriptomics) analysis using QIAGEN...

Thu, 26 Feb 2026 17:46:53 GMT

This 90-minute training session will show you how QIAGEN Ingenuity Pathway Analysis (IPA) helps visualize molecular intricacies and variations at multiple levels, such as transcriptome, proteome and metabolome. Through a series of brief technical vignettes, we will demonstrate how to:

- Generate associations among molecular signatures obtained via integrating multi-omics data
- Extract mechanisms from multi-omics data for precision medicine
- Disease stratification based on multi-omics profiles
- Map disease networks among targets and indications

QIAGEN IPA new user training

Tue, 20 Jan 2026 10:43:58 GMT

Are you new to QIAGEN Ingenuity Pathway Analysis (IPA) or interested in expanding your skill set? Join us as we learn more on large dataset analysis and knowledge base queries using QIAGEN IPA.

You’ll learn to:

• Upload multiple dataset types (e.g., RNA-seq, proteomics, metabolomics) and perform interactive core/pathway analysis in IPA

• Learn how to interpret different results, including pathways, key regulators, impact on biological functions/diseases and more

• Compare different experimental conditions (e.g., single-cell clusters, disease types) and identify similarities and contrasts

• Generate a network for hypothesis generation, even without a dataset or experimental design

Already have an IPA license? Install IPA and start using it now:

https://qiagen.showpad.com/share/CBv30blCPKFDUYHRWtAvI

Learn more about IPA or request a free trial:https://digitalinsights.qiagen.com/ipa

Automating insights: Scalable pathway analysis using the QIAGEN IPA APIs

Fri, 09 Jan 2026 09:43:49 GMT

As ‘omics datasets grow in size and complexity, automation becomes essential for efficient data interpretation. QIAGEN Ingenuity Pathway Analysis (IPA) is mainly accessed through its desktop client, but it has APIs – powerful tools that enable programmatic access to IPA’s functionalities.

Explore seamless integration of IPA into your bioinformatics pipelines, automate repetitive tasks and scale your pathway analysis across multiple datasets. Whether you are working in drug discovery, toxicology or translational research, IPA’s APIs can help accelerate your insights and improve reproducibility.

· Overview of QIAGEN Ingenuity Pathway Analysis

· Learn how to upload datasets, run core analyses and retrieve results programmatically

· Display a Gene View based on a gene ID

· Show the findings that connect two molecules

· Send a set of genes into IPA to automatically create a pathway

Investigating genomic variants using QIAGEN CLC Genomics Workbench, QCI...

Thu, 08 Jan 2026 10:40:11 GMT

Discovery of new genes implicated in hereditary diseases or cancer progression is challenging and advancing rapidly with an increase in the amount of cohort data to analyze from next generation sequencing (NGS) data to associations between gene variants and diseases, and finally to biological mechanisms of these gene variants. Combining QIAGEN CLC Genomics Workbench, QCII-T, and IPA, scientists can analyze sequencing data obtained from a variety of NGS technologies, annotate gene variants using the world’s most comprehensive and up-to-date curated scientific evidence, and find biological connections in gene variants with manually curated scientific findings. Get valuable and reliable insights for your research project and speed up your discoveries by using a streamlined NGS analysis workflow.

In this webinar, attendees will have the opportunity to:

1. Learn how to import whole genome or exome sequencing data into QIAGEN CLC Genomics Workbench and use the ultra-fast LightSpeed Module that delivers end-to-end NGS FASTQ to VCF pipeline;

2. Explore capabilities in QCII-T which can enable scientists to accelerate discoveries from hereditary or tumor cohort analyses to find associations between gene variants and diseases;

3. Learn how to use IPA and its manually curated content among other integrated scientific evidence to uncover novel biological mechanisms underlying these gene variants.

Unlock Biological Insights for Bioengineering using QIAGEN IPA

Fri, 12 Dec 2025 18:25:00 GMT

Explore how QIAGEN Ingenuity Pathway Analysis (IPA) can accelerate bioengineering research by powering insights into molecular mechanisms, signaling pathways and gene networks. Whether you are working on synthetic biology, tissue engineering or biomaterials, IPA helps translate ‘omics data into actionable biological understanding. See how you can use IPA to design experiments, interpret complex datasets and uncover novel therapeutic targets.

• Understand how IPA supports transcriptomics, proteomics and metabolomics data interpretation.

• Learn how to identify key regulators, canonical pathways and molecular interactions relevant to bioengineering applications.

• Discover how to predict upstream drivers and downstream effects of gene expression changes.

• See how IPA can guide hypothesis generation and experimental planning.

• Explore real-world applications of IPA in synthetic biology, regenerative medicine and biomaterials development.

Connected discovery: Scaling IPA insights across your organization

Fri, 12 Dec 2025 08:58:57 GMT

Accelerate discovery by transforming how your team collaborates with QIAGEN Ingenuity Pathway Analysis (IPA). You already know that IPA helps scientists rapidly interpret the causal biology behind their data—identifying upstream regulators, pathways, and mechanistic networks with ease. In this 45-minute vision-generating session, we’ll demonstrate how enterprise-level features in IPA can help your organization move from isolated analyses to a connected, insight-driven discovery engine.

Attendees will learn how to:

• Automate data integration using the IPA Upload API to seamlessly send differential expression results and trigger Core Analyses—making IPA a routine part of your analysis pipeline.

• Streamline collaboration with Collaborative Workspaces (CWS), where team members can automatically access shared results without manual coordination.

• Leverage collective knowledge through Analysis Match, which compares new results against your organization’s entire library of analyses—surfacing relevant compounds, disease models, or experimental signatures in seconds.

Whether you're scaling up internal screening efforts or aligning cross-functional teams, this webinar will show how IPA can unify your data and accelerate your path to discovery.

New user training: Large dataset analysis and knowledge base queries using...

Tue, 09 Dec 2025 21:10:32 GMT

Join us for a 90-minute training session for new users of QIAGEN IPA. Users will learn how to: • Upload their dataset (RNA-seq, scRNA-seq, proteomics, metabolomics and more) and perform interactive core/pathway analysis in IPA • Understand the different result types produced (pathways, key regulators, impact on biological functions/diseases and more) • Compare different experimental conditions (treatments, timepoints, single-cell clusters, disease types and more) and identify similarities and contrasts • Generate a network even without a dataset or experimental design for hypothesis generation

QIAGEN IPA deep-dive and new features training, America - Nov 3 2021

Tue, 09 Dec 2025 21:10:03 GMT

As requested by many users, your QIAGEN Digital Insights team is excited to introduce QIAGEN Ingenuity Pathway Analysis (IPA) deep-dive trainings. In these three-hour training sessions, we will discuss the following topics:

Part 1: Deep dive into QIAGEN IPA core and comparison analyses

Part 2: Deeper dive into how to use QIAGEN IPA even without user data

From Signature to Strategy: Drug Repurposing and Indication Expansion with...

Mon, 24 Nov 2025 11:37:10 GMT

Discover how QIAGEN Ingenuity Pathway Analysis (IPA) and OmicSoft Studio empower researchers to uncover hidden synergies within their existing drug portfolios. Whether you're exploring new indications or repurposing known compounds, these tools provide a data-driven framework to accelerate discovery and reduce development costs.

Learn how to:

• Diagram their current pipeline of drugs, targets and indications using IPA’s network construction and overlay tools

• Introduce a new gene signature and assess its interaction with known targets and pathways

• Query curated real-world datasets from OmicSoft Lands to validate predicted interactions and uncover novel therapeutic opportunities

• Compare gene profiles against disease vs. normal datasets to identify candidates for indication expansion

Join us to see how integrating deeply curated ‘omics data with predictive analytics can transform your drug development strategy.

Single-cell RNA-seq data interpretation using QIAGEN IPA

Thu, 13 Nov 2025 16:22:19 GMT

In this webinar, the speaker will go over how to:

• Identify critical pathways and networks in your single cell data, giving you insight into biological mechanisms

• Discover novel regulators, master regulators and biomarkers associated with different cell types

• Compare different cell clusters through pathways/networks activity heatmap to understand differences between your cell types or experimental groups

• Generate interactive IPA Interpret reports for sharing and collaboration

• Export high resolution images and tabular results for posters, publications and biopharma reports

‘Omics to Insights: Leveraging QIAGEN IPA for Pre-Clinical Toxicology and...

Thu, 13 Nov 2025 11:31:24 GMT

Pre-clinical toxicology studies generate complex datasets that require robust interpretation to identify potential safety liabilities early in drug development. QIAGEN Ingenuity Pathway Analysis (IPA) can help uncover mechanistic insights, predict toxicity outcomes and support decision-making in pre-clinical safety assessments. Explore how you can apply IPA to ‘omics data to identify toxicity signatures, understand mode of action (MoA) and prioritize biomarkers.

· Overview of QIAGEN Ingenuity Pathway Analysis

· Find transcriptomic and proteomic data from pre-clinical and clinical studies and gain mechanistic insights using OmicSoft Explorer and Ingenuity Pathway Analysis

· Visualize and interpret complex biological relationships that may be behind toxicity mechanisms using network construction

· Prioritize candidate biomarkers for safety monitoring using biomarker tools and OmicSoft Land Explorer

QIAGEN IPA New User Training

Thu, 13 Nov 2025 09:16:13 GMT

Are you new to QIAGEN Ingenuity Pathway Analysis (IPA) or interested in expanding your skill set? Join us as we learn more on large dataset analysis and knowledge base queries using QIAGEN IPA.

You’ll learn to:

• Upload multiple dataset types (e.g., RNA-seq, proteomics, metabolomics) and perform interactive core/pathway analysis in IPA

• Learn how to interpret different results, including pathways, key regulators, impact on biological functions/diseases and more

• Compare different experimental conditions (e.g., single-cell clusters, disease types) and identify similarities and contrasts

• Generate a network for hypothesis generation, even without a dataset or experimental design

Already have an IPA license? Install IPA and start using it now:

https://qiagen.showpad.com/share/CBv30blCPKFDUYHRWtAvI

Learn more about IPA or request a free trial: https://digitalinsights.qiagen.com/ipa

Investigating biomarkers with bulk and single-cell RNA-seq expression data

Wed, 29 Oct 2025 15:55:53 GMT

QIAGEN Ingenuity Pathway Analysis (IPA) is designed to help you analyze and compare different types of 'omics data. In this webinar, we’ll compare bulk RNA-seq and single-cell RNA-seq data to identify common regulators/targets and see how those regulators/targets associate with your phenotype of interest. We will also use sample-level public data to validate gene expression of common genes in tissues and/or cell type of interest.

You'll learn how to:

Generate a Comparison Analysis for bulk and single-cell RNA-seq
Identify significant common genes with the Compare feature
Build a custom network associating common genes to a phenotype
Examine sample- and cell-level expression in OmicSoft content

Spatial ‘omics meets network biology: Actionable insights into target and...

Wed, 22 Oct 2025 13:28:33 GMT

Discover actionable drug targets in your spatial transcriptomics data with systems biology and network analysis.

In this 60-minute session, we’ll start with differential expression data and explore ways to derive biological insights across experimental observations. Then, we’ll investigate and compare these findings across other harmonized and curated data.

We’ll show you how to:

Identify regions of interest in oral squamous cell carcinoma biopsies
Generate new networks by connecting genes to functional hallmarks of cancer
Predict upstream regulators and activity in a custom network with new causal analysis on the fly features
Test potential drug targets with in-silico experimentation
Overlay data and save custom network patterns of interest for causal scoring in future experiments
Explore other indications and potential treatments with curated, harmonized data

Find out what happens when spatial ‘omics data meets network biology.

QIAGEN IPA new user training

Wed, 22 Oct 2025 13:01:01 GMT

Are you new to QIAGEN Ingenuity Pathway Analysis (IPA) or interested in expanding your skill set? Join us as we learn more on large dataset analysis and knowledge base queries using QIAGEN IPA.

You’ll learn to:

• Upload multiple dataset types (e.g., RNA-seq, proteomics, metabolomics) and perform interactive core/pathway analysis in IPA

• Learn how to interpret different results, including pathways, key regulators, impact on biological functions/diseases and more

• Compare different experimental conditions (e.g., single-cell clusters, disease types) and identify similarities and contrasts

• Generate a network for hypothesis generation, even without a dataset or experimental design

Already have an IPA license? Install IPA and start using it now: https://qiagen.showpad.com/share/CBv30blCPKFDUYHRWtAvI

Learn more about IPA or request a free trial: https://digitalinsights.qiagen.com/ipa

IPA Interpret: A hands-on workshop

Thu, 02 Oct 2025 17:05:24 GMT

You will learn how to:

• Create an IPA Interpret report that can be easily shared with others

• Gain valuable insight into critical biological pathways, key regulators and more with just a few clicks

• Easily customize charts, such as the highly popular volcano bubble chart, taking advantage of new features introduced with recent updates

• Export both graphical and tabular results

Please make sure you can open the following IPA interpret report for this hands-on workshop:

https://analysis.ingenuity.com/ipw/RVy_DS08o_2CDODA-BNBIg

Please feel free to reach out to us if you run into any issues.

QIAGEN Ingenuity Pathway Analysis (IPA) for grant writing and publications

Mon, 15 Sep 2025 11:16:40 GMT

You'll learn how to:

• Search IPA’s vast collection of curated literature and omics data

• Build your own networks and predict activity changes

• Effectively use new features such as IPA Interpret for collaboration and hypothesis generation

• Explore a library of over 100,000 precomputed IPA analyses pulled from publicly available studies

• Deeply interrogate critical pathways

• Predict regulators causing your observed expression changes

• Contextualize your results by comparing them to internal and public data

• Generate the necessary tables and figures for your manuscript

IPA deeper dive - miRNA investigation using QIAGEN Ingenuity Pathway Analysis

Fri, 29 Aug 2025 10:00:20 GMT

In this webinar, you will learn how to use QIAGEN Ingenuity Pathway Analysis to identify target mRNAs for your miRNAs of interest and associate them with pathways, diseases, biological functions, tissues and cell types.

Explore:

• How to analyze miRNA-seq datasets alone or together with the corresponding mRNA datasets

• How to use QIAGEN IPA without a dataset, using miRNA IDs

• An introduction to databases and curated content specific to miRNA

• How to effectively apply various filters and functionalities to identify biomarkers, key targets and biological mechanisms

Public single-cell expression data made easy with QIAGEN IPA

Mon, 25 Aug 2025 16:04:33 GMT

Many QIAGEN Ingenuity Pathway Analysis (IPA) users have expressed strong interest in taking advantage of public single-cell expression data. Such data is readily available and easily accessible in IPA. We are hosting a 1hr training focused on some common use cases related to this topic.

You'll learn to:

• Easily locate single-cell studies, samples or cell types of interest

• Study pathways and networks pertaining to such projects to explore biological and cellular mechanisms

• Investigate sample- and cell-level gene expression for biomarker investigation

Discovery from public oncological data using QIAGEN Omicsoft OncoLand and...

Mon, 25 Aug 2025 10:45:20 GMT

In this 90-minute training, we will discuss how to discover and validate biomarkers as well as drug targets and key genes using public oncological data from GEO, TCGA, CCLE and other sources. To do this, we will use QIAGEN Omicsoft OncoLand, QIAGEN Ingenuity Pathway Analysis (IPA) and the OmicSoft Land Explorer web interface.

Specifically, for conditions of interest (diseases, cell lines, treatments etc.), we will discuss how to:
• Identify public studies of interest
• Derive a biomarker/gene signature
• Study expression of a gene or drug target
• Correlate expression of multiple genes and biomarkers
• Visualize a gene signature in the context of a heatmap
• Compare public data with other public data or a user’s own data

Speaker: Sumana Chintalapudi, Ph.D., Field Application Scientist, QIAGEN Digital Insights

Shared Pathways, Many Origins: How Diverse Genetic Risk Targets Share...

Wed, 20 Aug 2025 15:57:37 GMT

Over two decades of research have uncovered over 100 genes with rare mutations linked to autism spectrum disorder (ASD), yet transcriptomic and epigenetic analyses reveal convergent dysregulation patterns in ASD brain tissue. In this webinar, learn how Dr. Dan Geschwind and his team at UCLA combine bioinformatics and experimental approaches to show that both common and rare genetic variations converge during early fetal cortical development. Using the largest hiPSC patient cohort and cortical organoid models, they identified shared transcriptional changes and created a resource of isogenic lines with over 100 ASD-associated mutations. Their integrative, network-based approach aims to clarify how genetic risk influences neurodevelopment through transcriptional regulation.

Speaker: Dan Geschwind, MD, PhD

Gordon and Virginia MacDonald Distinguished Professor of Neurology, Psychiatry and Human Genetics

Senior Associate Dean and Associate Vice Chancellor of Precision Health, Institute for Precision Health (IPH)

University of California Los Angeles (UCLA)

IPA Webinar: Part 3: Search and Explore in IPA

Tue, 19 Aug 2025 10:17:49 GMT

IPA has broadly been adopted by the life science research community and is cited in thousands of articles for the analysis, integration, and interpretation of data derived from ‘omics experiments, such as RNA-seq, small RNA-seq, microarrays including miRNA and SNP, metabolomics, proteomics, and small scale experiments. Hosted by two QIAGEN Senior Scientists, this series will show you step-by-step how to implement and use IPA to get the most out of your data.

Part 3: Search and Explore in IPA

Learn how IPA’s knowledge and discovery tools can accelerate your research with the use of recent literature findings and assistance in hypothesis generation. This webinar will describe how to explore inter-related information about genes, biological pathways and more using interactive and customized tools. Leverage this information instantly without needing to upload your data.

Interested in learning more or trying IPA? Click here.

IPA Webinar: Part 1: Introduction to Ingenuity Pathway Analysis

Tue, 19 Aug 2025 10:17:07 GMT

Learn how to quickly and easily identify significant pathways, discover potential novel regulatory networks, and get the most out of your 'omics data!

Part 1: Introduction to the IPA Core Analysis

Learn how to view and interpret Core Analysis results in IPA, which allows you to relate the molecules in your dataset to information in the QIAGEN Knowledge Base. You will learn how to:

Uncover signaling and metabolic canonical pathways enriched in your data
Predict activation or inhibition of upstream regulators
Identify biological functions and diseases that are predicted to be increasing or decreasing
Generate causal hypotheses
Build networks describing potential molecular interactions of your dataset molecules
Compare your analyses to thousands of analyses created from public datasets

Interested in learning more or trying IPA? Click here.

Summer 2025 IPA Interpret and OmicSoft Explorer Enhancements

Mon, 18 Aug 2025 22:47:50 GMT

Join us to review exciting new features in IPA Interpret and OmicSoft Explorer.

We will walk though the latest enhancements in IPA Interpret like:

• Bubble charts for various analysis results

• Customizing charts

• More context for Graphical Summary results

• Explore matching and anti-matching datasets easily with more details

We will also walk through how to explore gene signatures in OmicSoft Explorer. You can readily find other experiments that match or anti-match your prescribed list of genes and expression patterns.

QIAGEN IPA new user training

Tue, 12 Aug 2025 22:47:00 GMT

Are you new to QIAGEN Ingenuity Pathway Analysis (IPA) or interested in expanding your skill set? Join us as we learn more on large dataset analysis and knowledge base queries using QIAGEN IPA.

You’ll learn to:

• Upload multiple dataset types (e.g., RNA-seq, proteomics, metabolomics) and perform interactive core/pathway analysis in IPA

• Learn how to interpret different results, including pathways, key regulators, impact on biological functions/diseases and more

• Compare different experimental conditions (e.g., single-cell clusters, disease types) and identify similarities and contrasts

• Generate a network for hypothesis generation, even without a dataset or experimental design

Already have an IPA license? Install IPA and start using it now:

https://qiagen.showpad.com/share/CBv30blCPKFDUYHRWtAvI

Learn more about IPA or request a free trial: https://digitalinsights.qiagen.com/ipa

IPA deeper dive - Making the most out of core expression analysis

Tue, 12 Aug 2025 22:45:39 GMT

A core/expression analysis is performed for RNA-seq, scRNA-seq, proteomics and many other types of ‘omics data. Driven by high demand from new user training sessions, we will dive into the details around a core analysis and its results.

Answer questions such as:

• What are the different result types produced by an IPA core analysis?

• How can we identify key regulators and relevant regulatory networks?

• What are the biomarkers and genes associated with diseases and biological processes of interest?

• Can IPA help generate novel directional (regulator effects) and non-directional (interaction) networks from a user’s dataset?

Come with your questions, and we'll address them during the webinar.

If you haven’t done a core/expression analysis in IPA before, we recommend you review the slides below before (or after) this training. It’s not a requirement, but it will help.

https://qiagen.showpad.com/share/SQjinvdxIs1iGhL8H3eOd

Slide#4 = how to download the example dataset

Slide#20 -25 = review recommended dataset formats

Slide#53 onwards = step-by-step how to upload the dataset and perform analysis

o Install IPA: https://qiagen.showpad.com/share/A0mV7EWcejBtXPJUesbXd

o IPA beginner training recording:

https://qiagen.showpad.com/share/Dcdg28jxw0D2uRpgRqFK4

Accelerating biomarker signature discovery for rare diseases using curated...

Tue, 12 Aug 2025 22:44:11 GMT

Identifying molecular signatures for rare diseases is challenging, mainly due to limited sample sizes and heterogenous data. Researchers must often piece together fragmented evidence to uncover shared biological mechanisms. Though inescapable, this process can be more efficient.

See how QIAGEN OmicSoft Lands and Ingenuity Pathway Analysis (IPA) streamlines biomarker signature discovery using curated real-world datasets and powerful causal analytics. With automation powered by SQL, Python and R APIs, OmicSoft and IPA enable scalable, reproducible analyses across multiple disease contexts, accelerating the path from data to discovery.

You will learn how to:

• Explore and query neurodegenerative disease datasets in QIAGEN OmicSoft Lands using SQL and Python

• Automate pathway and regulator analysis in IPA using Python and R APIs

• Scale and produce analyses across multiple cohorts

IPA Interpret graphical summary

Mon, 11 Aug 2025 12:07:01 GMT

The Graphical Summary in IPA Interpret has been made more informative and easier to interpret. In Upstream Regulators, you can easily see the dataset details for genes in the summary. A tooltip now provides information about the Upstream Regulator’s score from your analysis and expression details (if the gene is in your dataset). This way, you can evaluate the expression of the underlying gene and view its prediction as a regulator at the same time.

IPA Interpret bubble charts

Mon, 11 Aug 2025 12:06:45 GMT

New in IPA Interpret, bubble charts can help you find interesting patterns in your results, focus on the most important predictions and create compelling visualizations for presentation and publications.

IPA Interpret bar charts

Mon, 11 Aug 2025 12:06:21 GMT

IPA Interpret now offers extensive customization of bar charts when exporting them as images. You can easily change the bar spacing, thickness and color, fonts and more. After you have filtered out non-relevant bars from your chart (if desired), click the export button and choose “Custom styling before download” from the menu that appears.

IPA Webinar: Part 2: Formatting and Uploading Your Dataset into IPA

Thu, 10 Jul 2025 21:46:14 GMT

Part 2: Formatting and Uploading Your Dataset into IPA

Learn how to format your own data and upload it into IPA so that you can perform pathway visualization and various different types of analyses. Learn how to:

• Format and upload the data to be analyzed by IPA

• Explore your uploaded data and start an analysis

Interested in learning more or trying IPA? Click here.

Upload differential expression file from single cell data to QIAGEN IPA

Thu, 10 Jul 2025 13:37:04 GMT

In this video, we will review how to export data from CELLxGENE and similar single cell portals to analyze in QIAGEN IPA for deeper biological insights.

IPA causal scoring

Wed, 09 Jul 2025 10:18:47 GMT

In the IPA desktop app, you can rapidly interrogate any pathway or network to discover relevant entities that may causally impact (or are impacted by) molecules on the pathway or network. This enables you to explore and generate hypotheses much faster than ever before in IPA. For example, you could discover upstream chemical inhibitors of a pathway of interest, find pathways that are likely inhibited by the activation of another, or explore how upstream drivers can lead to downstream outcomes.

Share IPA Interpret Analyses

Thu, 03 Jul 2025 15:46:50 GMT

IPA Interpret identifies and summarizes the biological themes in your results with the help of AI, creating a shareable, interactive report.

In this video, we’ll walk you through how to share analyses created in IPA Interpret.

Want to learn more? Visit us at https://digitalinsights.qiagen.com/products-overview/discovery-insights-portfolio/analysis-and-visualization/qiagen-ipa/qiagen-ipa-interpret/

Part III: Formatting and Uploading Your Data into IPA

Tue, 01 Jul 2025 11:40:01 GMT

Learn how to format your own data and how to upload it into IPA. IPA can upload your experimental data to enable you to perform pathways visualization, literature searches on the molecules in the dataset, and enable you to perform the many different type of analyses offered in IPA. In this webinar we will use metastatic melanoma microarray data as an example dataset.

Learn how to:
• Format the incoming data to be analyzed by IPA
• Upload the data for analysis
• Explore your uploaded data
• Start a Core Analysis

Sections:

Minutes Description

0:00-2:08 Introduction to the webinar

2:09-3:06 Description of the dataset used for the demonstration

3:07-7:17 Rules for formatting the dataset

7:18-9:44 Data measurements values that can be used

9:45-11:24 Additional formatting rules and potential issues

11:25-12:47 How to import Cuffdiff files

12:48-14:48 Where you can upload data in IPA

14:49-15:12 Navigating to the dataset

15:13-17:40 Dataset upload options

17:41-22:45 Mapping columns in the Raw Data view

22:46-24:03 Adding metadata

24:04-24:35 Saving the dataset

24:36-29:57 Creating Core Analysis settings

29:58-31:14 Previewing the dataset

31:15-35:10 Setting cutoffs

35:11-38:41 Starting the analysis and Summary

38:42-39:41 Upcoming webinars

39:42 to end How to contact us

Interpreting your comparison analyses results in IPA

Mon, 30 Jun 2025 13:40:21 GMT

Learn how to view and interpret your comparison analyses results in IPA and the multiple ways of relating the molecules in your dataset to the body of information in the Ingenuity Knowledge Base. IPA allows you to compare analysis results from multiple experimental groups to identify similarities, differences, and trends. Heatmaps for Canonical Pathways, Upstream Regulators, and Diseases & Functions allow you to easily and quickly view information from your analyses side-by-side. You can also visualize Gene Heatmaps to gain instant insight into specifically how genes affect your results.

Interpreting the Results of Your Phosphoproteomics Analysis in IPA

Mon, 30 Jun 2025 13:38:38 GMT

Learn how to view and interpret your Phosphoproteomics Analysis results in IPA. Find out how to understand your Phosphoproteomics Analysis and about the multiple ways of relating the molecules in your dataset to the body of information in the Ingenuity Knowledge Base.

Interested in learning more?

Click here

New user training: QIAGEN Ingenuity Pathway Analysis (IPA)

Mon, 30 Jun 2025 13:31:46 GMT

New user training: Large dataset analysis and knowledge base queries using QIAGEN Ingenuity Pathway Analysis (IPA)

Users will learn how to:
• Upload their dataset (RNA-seq, scRNA-seq, proteomics, metabolomics and more) and perform interactive core/pathway analysis in IPA
• Understand the different result types produced (pathways, key regulators, impact on biological functions/diseases and more)
• Compare different experimental conditions (treatments, timepoints, single-cell clusters, disease types and more) and identify similarities and contrasts
• Generate a network even without a dataset or experimental design for hypothesis generation

Uncover molecular drivers of the tumor microenvironment using curated data...

Fri, 27 Jun 2025 08:36:13 GMT

Understanding the tumor microenvironment (TME) presents a major challenge for biopharma researchers and translational scientists. The complexity of cellular interactions, variability across patient samples, and overwhelming volume of public omics data can make it difficult to pinpoint key molecular drivers and predict functional consequences. Building a clear, actionable view of the TME often feels like assembling a puzzle without the picture on the box.

In this webinar, discover how QIAGEN Ingenuity Pathway Analysis (IPA) can help overcome these challenges by combining expertly curated biological knowledge with powerful predictive modeling tools. Learn how to easily construct molecular networks, interpret gene expression data from resources like TCGA and GEO, and model upstream regulators to predict immune and tumor behavior. Using examples such as IL1B’s role in non-small cell lung cancer (NSCLC), we’ll show you how IPA can accelerate your discoveries and guide therapeutic insights.

What you’ll learn:

How to identify disease-associated molecules and visualize their biological interactions
How to mine and interpret public gene expression data for deeper insights into cancer biology
How to model upstream regulators and predict functional outcomes within the TME

Multi-omics (metabolomics, proteomics, transcriptomics) analysis using QIAGEN...

Fri, 27 Jun 2025 08:30:09 GMT

This 90-minute training session is about how QIAGEN Ingenuity Pathway Analysis (IPA) allows visualization of molecular intricacy and variations at multiple levels such as transcriptome, proteome, and metabolome. Through a series of brief technical vignettes, it is demonstrated how to:

· Generate associations among molecular signatures obtained via integrating multi-omics data

· Extract mechanisms from multi-omics data for precision medicine

· Disease stratification based on multi-omics profiles

· Map disease networks among targets and indications

QIAGEN IPA Summer Camp - Day 3

Fri, 13 Jun 2025 13:37:39 GMT

Join us for three 60-minute training sessions for QIAGEN Ingenuity Pathway Analysis (IPA).

In this training, you’ll learn how to:

Monday June 9 – Session#1: 1pm ET/10am PT • IPA general overview • Upload your dataset (RNA-seq, scRNA-seq, proteomics, metabolomics and more) • Set up core/pathway analysis in IPA

Tuesday June 10 – Session#2: 1pm ET/10am PT • Understand the different result types produced (pathways, key regulators, and more) • Customize chart outputs using filters and different chart types like a volcano plot like bubble chart

Wednesday June 11 – Session#3: 1pm ET/10am PT • Compare different experimental conditions (different ‘omics data, treatments, time points, single-cell clusters, disease types and more) and identify similarities and contrasts • Generate a network even without a dataset or experimental design for hypothesis generation

If you are able to attend, then we will have additional scientists on the call for Q&A. If you are unable to attend, registering will still allow you to view the recordings.

QIAGEN IPA Summer Camp - Day 2

Fri, 13 Jun 2025 12:04:38 GMT

Join us for three 60-minute training sessions for QIAGEN Ingenuity Pathway Analysis (IPA).

In this training, you’ll learn how to:

Monday June 9 – Session#1: 1pm ET/10am PT • IPA general overview • Upload your dataset (RNA-seq, scRNA-seq, proteomics, metabolomics and more) • Set up core/pathway analysis in IPA

If you are able to attend, then we will have additional scientists on the call for Q&A. If you are unable to attend, registering will still allow you to view the recordings.

QIAGEN IPA Summer Camp - Day 1

Thu, 12 Jun 2025 20:40:27 GMT

Join us for three 60-minute training sessions for QIAGEN Ingenuity Pathway Analysis (IPA).

In this training, you’ll learn how to:

Monday June 9 – Session#1: 1pm ET/10am PT • IPA general overview • Upload your dataset (RNA-seq, scRNA-seq, proteomics, metabolomics and more) • Set up core/pathway analysis in IPA

If you are able to attend, then we will have additional scientists on the call for Q&A. If you are unable to attend, registering will still allow you to view the recordings.

Venn diagrams and merging datasets using QIAGEN Ingenuity Pathway Analysis (IPA)

Thu, 22 May 2025 14:33:32 GMT

Based on recent feedback, we are hosting this 60 minute training focused on below 3 topics.

• How to increase memory in IPA for better loading of charts and networks (request from new users)

• How to generate Venn diagrams (request from new and experienced users)

• How to merge multiple datasets into a single file

Time and interest permitting, we are happy to cover other topics as well.

Beyond discovery_Invest in your research with QIAGEN

Thu, 22 May 2025 10:14:08 GMT

It’s a tough time to be in research, but QIAGEN is committed to bringing more insights to your work, no matter what challenges you face.

Start investing in your research with our new features, OmicSoft Explorer and IPA Interpret. You can unearth research gold in our curated collection of ‘omics datasets, explore detailed pathway analysis reports and share your insights with anyone with a computer.

In this webinar, you'll learn how to:

• Search through our collection of ‘omics datasets (RNA-seq, scRNA-seq, etc.) curated from GEO, SRA, TCGA and more, based on your criteria

• Examine project details like experimental setup and sample metadata

• Identify biomarkers associated with conditions of interest

• Share pathway analysis reports and insights into disease pathology, drug mechanism of action, cellular processes and more

Also, you’ll receive live answers to any questions you have during the live webinar.

Compare and contextualize results using QIAGEN Ingenuity Pathway Analysis

Thu, 24 Apr 2025 15:31:20 GMT

Take your IPA analysis results to the next level by comparing them to your own analyses (different timepoints, treatments, cell lines, diseased and more) or from a library of over 160,000 pre-computed datasets to find similar or opposite biological signatures. Identify key genes or entities and then explore how they are expressed across normal tissues, diseases and more from over 600,000 biological samples to gain deep context.

Attendees will learn how to:

• Use and interpret the IPA Activity Plot feature to identify key genes and regulators common across datasets

• Scan across pre-computed datasets to query for any collection of genes in a network or pathway for similar or opposite gene signature using Pattern Search

• Advance insights with the IPA Analysis Match comparison feature to compare large numbers of user datasets and/or public datasets (from GEO, SRA, cancer collections and more)

Biomarkers investigation through deep curated ‘omics data available through...

Tue, 22 Apr 2025 07:58:42 GMT

QIAGEN OmicSoft Lands allows in-depth investigation of biomarkers through deep curated high quality sample level gene and protein expression data obtained through diverse data sources (GEO, CPTAC, TCGA, GTEx and more). These lands are accessible through Ingenuity Pathway Analysis Explorer feature.

In this training the trainer will go over below workflow (designed based on user questions).

• Easily locate expression data of interest (pertaining to a disease, treatment, cell type etc.)

• Generate expression, correlation and other plots for biomarker investigation and conveniently customize them

• For various comparisons (example disease vs normal, response vs no response) perform pathways interpretation through IPA Interpret

• Conveniently export or share results

QIAGEN Ingenuity Pathway Analysis - ID mapping strategies

Wed, 16 Apr 2025 16:42:10 GMT

While Ingenuity Pathway Analysis (IPA) accepts wide range of identifiers (gene, transcript, protein, miRNA, metabolite and more) and allows easy mapping/upload of these identifiers, select identifiers require some work before they can be uploaded. In this training, the trainer will use locus tags for a Chinese Hamster Ovary (CHO) cell line dataset as an example to show how such IDs can be made more compatible for optimal mapping in IPA. The trainer will go over strategies such as

• Converting such IDs to GenePept IDs to greatly improve mapping

• Using Excel's XLOOKUP function to make seamless conversion.

• Incorporating metabolomic identifiers using publicly available tools

While CHO IDs are used as an example for this training, these strategies can be applied to other IDs as well.

Unlock insights with QIAGEN IPA: Compare, match and visualize curated...

Wed, 16 Apr 2025 09:19:00 GMT

Streamline your research with QIAGEN IPA and access over 200,000 expert-curated analyses from publicly available datasets. This webinar introduces three powerful methods to integrate these datasets with your own research, enhancing discovery and interpretation:

• Analysis Match: Automatically find analyses and datasets with comparable or contrasting biological results to validate your findings or uncover unexpected and shared mechanisms

• Pattern Search: Match your gene patterns or networks against the Analysis Match collection and find relevant datasets

• Activity Plot: Explore the predicted activity of pathways, regulators and more across disease conditions, treatments and more

Don’t miss this opportunity to unlock actionable insights and strengthen your analyses with reliable data and cutting-edge tools.

Investigating mechanisms underlying disease pathology using HGMD and...

Wed, 16 Apr 2025 09:15:54 GMT

This webinar will focus on how Human Gene Mutation Database (HGMD) and Ingenuity Pathway Analysis (IPA) can be used together for investigating molecular mechanisms underlying disease pathology.

Specifically, the presenter will cover

• A brief introduction to HGMD and IPA

• Using HGMD to investigate genes and variants of interest

• Using IPA for constructing novel networks explaining disease pathology

• Easily export tabular and graphical results

QIAGEN IPA - Discoveries from deep curated public gene and protein expression...

Mon, 07 Apr 2025 20:28:28 GMT

This is a special session put together based on some of the questions we received in recent trainings. IPA allows you to take advantage of deep curate public data from sources such as GEO, GTEx, CPTAC, TCGA and more. This training will focus on below 2 questions mainly but possibly others we receive through the registration and during the live session.

1) How to locate pathway analysis of a deep curated public dataset? Example I am interested in 'disease vs normal' or 'treated vs untreated' or 'cell type 1 vs others' comparison from a study. How can I launch pathway analysis of such dataset through IPA project search?

2) I also want to investigate such studies and consortia at sample expression level. Example how is a specific gene or protein expressed in disease1 vs disease 2 vs normal tissue or treated vs untreated samples? For 2 genes can we generate a correlation plot?

The training may last only ~60min but reserving longer time in case we receive additional questions.

Network construction and customization in QIAGEN Ingenuity Pathway Analysis

Fri, 28 Mar 2025 00:11:15 GMT

Per attendees’ request from a recent training, we are hosting this in-depth training focused on how to effectively construct a network and easily modify it for both no dataset or dataset (RNA-seq, proteomics, etc.) in QIAGEN Ingenuity Pathway Analysis.

In this interactive training, attendees will learn:

• How to construct a network from scratch or open a network/pathway of interest from their own analysis or Ingenuity database

• How to effectively use tools present in build and overlay menu to add molecules (genes/proteins), chemicals, metabolites, biological processes/diseases and more of their interest • How to modify the network (ex. keep only specific type of relationship like activation, phosphorylation, protein-protein binding and more)

• Perform in silico prediction (ex. if a drug, siRNA or CRISPR were to reduce activity of a gene/protein, how will impact remaining genes/proteins/diseases on that network)

• Export high resolution graphics or tabular relationships and/or make the created network usable in future pathway analysis

Additional QIAGEN Digital Insights (QDI) scientists will be on the call to answer your questions and help with other inquiries such as how to install the software.

Easily search and interpret 'omics datasets using OmicSoft Explorer and IPA...

Tue, 25 Mar 2025 12:33:20 GMT

In this webinar, the trainer will cover a highly requested usecase using OmicSoft Explorer and IPA Interpret, two of the new features recently introduced to both QIAGEN IPA and OmicSoft customers.

Specifically, the trainer will go over how to

• Easily search for deep curated high-quality omics (RNA-seq, scRNA-seq etc.) datasets of interest based on user defined criteria (Disease name, drug treatment and more) curated from sources such as GEO, SRA, TCGA and more

• Explore project details to gain better understanding of experimental setup and sample metadata

• Study volcano plots to identify biomarkers associated with conditions of interest

• Generate sharable pathway analysis reports that provide insights into disease pathology, drug mechanism of action, cellular processes and more

IPA Interpret and OmicSoft Explorer are now available through both IPA and OmicSoft. Learn more: https://qiagen.my.salesforce-sites.com/KnowledgeBase/KnowledgeNavigatorPage?id=kA4Sc00000023mbKAA&categoryName=BioX

IPA deeper dive miRNA investigation using QIAGEN Ingenuity Pathway Analysis

Tue, 18 Mar 2025 10:01:11 GMT

Description: In this 90-minute training session, you will learn how to identify target mRNAs for your miRNAs of interest and associate them with pathways, diseases, biological functions, tissues and cell types.

Topics that will be covered include:

• How to analyze miRNA-seq datasets alone or both miRNA and corresponding mRNA datasets together

• How to use QIAGEN IPA without a dataset, using miRNA IDs

• Introduction to databases and curated content specific to miRNA

• How to effectively apply various filters and functionalities to identify biomarkers, key targets and biological mechanisms

To learn more about IPA or request for a trial: https://digitalinsights.qiagen.com/products-overview/discovery-insights-portfolio/analysis-and-visualization/qiagen-ipa/?cmpid=CM_QDI_DISC_042024webinars-miRNA

Interpretation of spatial transcriptomics data using QIAGEN Ingenuity Pathway...

Fri, 14 Mar 2025 22:07:15 GMT

This 90-minute training session is about how QIAGEN Ingenuity Pathway Analysis (IPA) allows visualization of molecular intricacy and variations that scientists aim to elucidate from spatial transcriptomics data. We will take spatially segmented differential expression data generated using spatial transcriptomics platforms and learn how to derive biological insights across multiple experimental observations. We will walk through the following during this training:

• How to upload your spatial transcriptomics data into IPA

• How to set up core analyses

• Generate a comparison analysis across spatially segmented experimental groups

• Examine canonical pathway and upstream regulator shared or differing biology across your segmented datasets

Multi-omics (metabolomics, proteomics, transcriptomics) analysis using QIAGEN...

Mon, 03 Mar 2025 22:17:59 GMT

· Generate associations among molecular signatures obtained via integrating multi-omics data

· Extract mechanisms from multi-omics data for precision medicine

· Disease stratification based on multi-omics profiles

· Map disease networks among targets and indications

Deeply curated single-cell RNA-seq data investigation using QIAGEN Omicsoft...

Thu, 27 Feb 2025 10:36:55 GMT

Single-cell RNA-sequencing (scRNA-seq) is widely used to investigate tissue heterogeneity, identify novel cell types, study pathogenic mechanisms, develop targeted therapy (including immunotherapy) and more. Accordingly, a tremendous amount of scRNA-seq data has been deposited to public domains like GEO.

In this training, you will learn how to

· Locate public single-cell studies of interest using QIAGEN Omicsoft Single Cell Lands

· Study different cell types by dimension reduction plots (for example, t-SNE, UMAP)

· Investigate expression of genes of interest across different cell types (Violin plots, overlay expression on cluster)

· Identify key pathways and regulators from scRNA-seq data using QIAGEN Ingenuity Pathway Analysis (IPA)

Introduction to IPA Interpret for QIAGEN IPA

Thu, 23 Jan 2025 16:03:35 GMT

Now you can access and share the interpretative power of IPA in an easy-to-consume format – without installing any extra software.

IPA Interpret identifies and summarizes the biological themes in your results with the help of AI, creating a shareable, interactive report.

To learn more, visit https://digitalinsights.qiagen.com/products-overview/discovery-insights-portfolio/analysis-and-visualization/qiagen-ipa/qiagen-ipa-interpret/

Introduction to IPA Interpret for QIAGEN IPA

Thu, 23 Jan 2025 16:02:26 GMT

Now you can access and share the interpretative power of IPA in an easy-to-consume format – without installing any extra software.

IPA Interpret identifies and summarizes the biological themes in your results with the help of AI, creating a shareable, interactive report.

To learn more, visit https://digitalinsights.qiagen.com/products-overview/discovery-insights-portfolio/analysis-and-visualization/qiagen-ipa/qiagen-ipa-interpret/

Understanding Regulator Effects and Interaction Networks in QIAGEN IPA

Mon, 16 Dec 2024 10:13:28 GMT

Not sure what to do with Regulator Effects and Interaction Networks in IPA? After you conduct an IPA Core Analysis on your ‘omic dataset (RNA-seq, scRNA-seq, proteomics, metabolomics and more), start using the Regulator Effects and Interaction Networks results to interpret your data and generate hypotheses.

We’ll cover:

- Regulator Effects: These causal and directional networks connect major regulators with downstream diseases and biological functions

- Interaction Networks: These networks focus on the interconnectivity of molecules (genes, proteins, metabolites etc.) in your dataset

IPA RAP Portal DEMO

Thu, 05 Dec 2024 15:08:34 GMT

Take the stress out of data analysis and fast-track your path to gene expression insights with our RNA-seq Analysis Portal. Go from FASTQ files to IPA’s pathway analysis insights in hours instead of days.Our portal supports analyses for 20 species using proven, published algorithms. The RNA-seq Analysis Portal is compatible with QIAseq and other major RNA library kits, so you can process FASTQ files from SRA, BaseSpace or your local repository.After processing and QC, you can push data directly to your IPA account* for biological interpretation.

Discovering and investigating gene signatures for biologists and data scientists

Tue, 26 Nov 2024 10:19:33 GMT

Our high-quality, comprehensive databases are designed for biologists, wet lab scientists, and data scientists alike. Whether you prefer a seamless graphical user interface (GUI) or prefer the flexibility of programmatic access (APIs), our solutions make complex data analysis easy and accessible.

Explore the most effective ways to access our databases, including:

1. QIAGEN Ingenuity Pathway Analysis: Analyze responder vs. non-responder data and export genes from activated or inhibited pathways

2. OmicSoft Studio: Identify significant tumor vs. normal differentially expressed genes (DEGs) with proteomics or transcriptomics

3. Biomedical KB and Neo4j: Identify connected pathways, perform page rank analytics, remove top toxicology hits and show top remaining genes activated or inhibited by known drugs

4. OmicSoft Lands APIs: Perform gene set enrichment analysis to identify other diseases

New feature Insights with IPA Interpret

Fri, 22 Nov 2024 13:17:53 GMT

Unlock actionable insights in your biological data by streamlining your data interpretation with IPA Interpret.

The newest feature of your trusted pathway analysis software, QIAGEN IPA, includes:

• Content powered by IPA's extensive, manually curated knowledge base and aided by AI

• Easy-to-share reports and updated visualizations to facilitate collaboration and dissemination of research findings

• Easy access from your favorite web browser, no additional software or hardware needed

New feature Navigating datasets with OmicSoft Explorer

Fri, 22 Nov 2024 11:54:06 GMT

Meet OmicSoft Explorer, a new feature included with your QIAGEN IPA/OmicSoft subscriptions. See how you can find ‘omics datasets to inform your next experiments or support your grant proposals.

With OmicSoft Explorer, you can:

• Search over 10,000 disease-relevant datasets for clinical, in vitro, normal tissue and more

• Reveal top differentially expressed genes from over 200,000 experiments

• Discover experiments that include your gene of interest

• Explore underlying biology through IPA Interpret

IPA Interpret

Tue, 19 Nov 2024 11:34:30 GMT

QIAGEN IPA let’s you Analyze, Compare, and Contextualize your data. Now with IPA Interpret leverage the power of AI and get a streamlined report on your differential expression analyses with key interpretations. Share your report with others and explore the updated graphics capabilities. Learn more: https://digitalinsights.qiagen.com/products-overview/discovery-insights-portfolio/analysis-and-visualization/qiagen-ipa/qiagen-ipa-interpret/

Discover biomarkers, validate targets and identify variants with QDI software

Tue, 19 Nov 2024 08:54:21 GMT

Learn how to leverage solutions from QIAGEN Digital Insights to discover biomarkers, validate targets, and identify variants.

Attendees will learn to:

1. Locate public studies of interest using OmicSoft DiseaseLand

2. Investigate expression of genes of interest across different treatments, disease states, etc.

3. Identify variants of interest for candidate biomarkers and targets using Human Gene Mutation Database (HGMD)

4. Leverage the QIAGEN Knowledgebase in Ingenuity Pathway Analysis (IPA) to explore and extend findings from OmicSoft DiseaseLand and HGMD

5. Access data from OmicSoft, HGMD and IPA in ways that are helpful for data scientists

Introducing the RNA-seq Analysis Portal in QIAGEN IPA

Mon, 21 Oct 2024 13:44:55 GMT

Get to know the RNA-seq Analysis Portal, a cloud-based platform you can access from within QIAGEN Ingenuity Pathway Analysis (IPA) that helps you analyze your RNA-seq expression data. Its predefined analysis pipelines let you calculate expression levels and identify differential expression and significant pathways, regulators, diseases and functions in just a few steps. The graphical views and interactive plots enable seamless exploration and refinement of your RNA-seq analysis results.

In this training you will learn how to

• Upload your own expression data (example raw FASTQ files) or start with a public dataset

• Perform RNA-seq analysis and generate outputs such as heatmap, differential expression table, volcano plot and more

• Export graphical and tabular results

Investigating biomarkers with bulk and single-cell RNA-seq expression data

Tue, 01 Oct 2024 12:35:52 GMT

You'll learn how to:

• Generate a Comparison Analysis for bulk and single-cell RNA-seq

• Identify significant common genes with the Compare feature

• Build a custom network associating common genes to a phenotype

• Examine sample- and cell-level expression in OmicSoft content

IPA RNA-Analysis Portal

Wed, 04 Sep 2024 14:26:54 GMT

Public single-cell expression data made easy with QIAGEN IPA

Fri, 30 Aug 2024 14:09:48 GMT

You'll learn to:

• Easily locate single-cell studies, samples or cell types of interest
• Study pathways and networks pertaining to such projects to explore biological and cellular mechanisms
• Investigate sample- and cell-level gene expression for biomarker investigation

IPA deep dive miRNA investigation using QIAGEN Ingenuity Pathway Analysis

Thu, 29 Aug 2024 11:22:20 GMT

In this 90-minute training session, you will learn how to identify target mRNAs for your miRNAs of interest and associate them with pathways, diseases, biological functions, tissues and cell types.

Topics that will be covered include:

• How to analyze miRNA-seq datasets alone or both miRNA and corresponding mRNA datasets together
• How to use QIAGEN IPA without a dataset, using miRNA IDs
• Introduction to databases and curated content specific to miRNA
• How to effectively apply various filters and functionalities to identify biomarkers, key targets and biological mechanisms

QIAGEN Ingenuity Pathway Analysis (IPA) for grant writing and publications

Sun, 18 Aug 2024 01:40:16 GMT

IPA is more than just an analysis program; it can also help you write grants and publications. IPA provides biological insights backed by expert-curated findings and thousands of pre-analyzed multi-omics datasets. You can search for existing knowledge on molecules of interest, build networks and review results from public studies. Or you can identify key pathways, regulatory molecules and functional changes in your results and see how your data relates to published studies.

You'll learn how to:
• Search IPA’s vast collection of curated literature and omics data
• Relate molecules to phenotypes and functions
• Build your own networks and predict activity changes
• Explore a library of over 90,000 precomputed IPA analyses pulled from publicly available studies
• Format your dataset and set up an analysis
• Deeply interrogate key Canonical Pathways
• Predict regulators causing your observed expression changes
• Contextualize your results by comparing them to internal and public data
• Generate the necessary tables and figures for your manuscript

Sharing your analysis results with others in QIAGEN IPA

Fri, 16 Aug 2024 11:34:48 GMT

QIAGEN Ingenuity Pathway Analysis (IPA) is a powerful tool that allows you to upload and analyze your 'omics data to identify key biological pathways and mechanisms and regulatory molecules. But did you know that you can share your analysis results with others? In this 60-minute webinar, we’ll explore the Share Manager and the Collaboration Workspace in IPA and go over the many ways you can share your analysis results with others or how they can share their results with you.

Attendees will learn how to:

• Share datasets and analysis with other IPA users
• Use the Share with me feature
• Email interactive pathways to other IPA users
• Use a Collaboration Workspace (CWS)

IPA deeper dive: Making most out of user’s core/expression analysis

Wed, 24 Jul 2024 15:19:56 GMT

An Ingenuity Pathway Analysis (IPA) deeper dive into the core analysis (also known as expression analysis) training was requested by IPA users. Core/Expression analysis is performed on RNA-seq, scRNA-seq, proteomics and many other types of ‘omics data). Accordingly, this training will focus on these topics and more:
· What are the different result types of results produced by an IPA core analysis?
· How can we identify key regulators and relevant regulatory networks?
· What are the biomarkers and genes associated with diseases and biological processes of interest?
· Can IPA help me generate novel directional (regulator effect) and non-directional (interaction) networks from user’s dataset?
· Another topic per registrant request

If you haven’t done a core/expression analysis in IPA before, we recommend you review the below slides before (or after) this training. It’s not a requirement for following this training but it will help.

Investigate biomarkers, drug targets and more with QIAGEN IPA BioProfiler

Wed, 17 Jul 2024 10:41:52 GMT

QIAGEN IPA's BioProfiler feature allows you to explore and filter the details behind the connections of molecules to diseases and biological functions.

You'll learn to use BioProfiler to:
· Make novel discoveries with the ability to filter the fine-grained relationships between molecules (genes, RNAs, proteins and chemicals) and diseases or functions
· Identify how specific genes are causally linked to user’s disease(s) of interest
· Investigate different types of biomarkers
· Investigate drugs in different phases of clinical trials
· Display molecules and their disease or function associations as a network

QIAGEN Ingenuity Pathway Analysis (IPA) summer camp Part 3

Wed, 17 Jul 2024 10:38:08 GMT

• Compare different experimental conditions (different ‘omics data, treatments, time points, single-cell clusters, disease types and more) and identify similarities and contrasts
• Generate a network even without a dataset or experimental design for hypothesis generation

QIAGEN Ingenuity Pathway Analysis (IPA) summer camp Part 2

Wed, 17 Jul 2024 10:37:05 GMT

• Understand the different result types produced (pathways, key regulators, and more)
• Customize chart outputs using filters and different chart types like a volcano plot like bubble chart

QIAGEN Ingenuity Pathway Analysis (IPA) summer camp Part 1

Wed, 17 Jul 2024 10:34:59 GMT

• IPA general overview • Upload your dataset (RNA-seq, scRNA-seq, proteomics, metabolomics and more)
• Set up core/pathway analysis in IPA

Venn diagram and merging datasets using QIAGEN Ingenuity Pathway Analysis (IPA)

Wed, 12 Jun 2024 14:07:22 GMT

Based on recent feedback, we are hosting this 60min training focused on below 3 topics.
• How to increase memory in IPA for better loading of charts and networks (request from new users)
• How to generate Venn Diagram (request from new and experienced users)
• How to merge multiple dataset files into a single file

Compare and contextualize results using Ingenuity Pathway Analysis

Thu, 30 May 2024 15:07:00 GMT

Attendees will learn how to:

• Use and interpret the IPA Activity Plot feature to identify key genes and regulators common across datasets
• Scan across pre-computed datasets to query for any collection of genes in a network or pathway for similar or opposite gene signature using Pattern Search
• Advance insights with the IPA Analysis Match comparison feature to compare large numbers of user datasets and/or public datasets (from GEO, SRA, cancer collections and more)

IPA deep dive: miRNA investigation using QIAGEN Ingenuity Pathway Analysis...

Thu, 02 May 2024 17:07:58 GMT

In this 90-minute training session, you will learn how to identify target mRNAs for your miRNAs of interest and associate them with pathways, diseases, biological functions, tissues and cell types.

Topics that will be covered include:

Network construction and customization with QIAGEN Ingenuity Pathway Analysis

Thu, 02 May 2024 08:20:00 GMT

This in-depth training focuses on effectively constructing a network, with or without a dataset (RNA-seq, proteomics, etc.), and easily modifying it – all within Ingenuity Pathway Analysis.

In this interactive training, attendees will learn how to:

• Construct a network from scratch or open a network/pathway of interest from their analysis or the Ingenuity Knowledge Base
• Effectively use tools present in the Build and Overlay menus to add molecules (genes/proteins, chemicals, metabolites), biological processes/diseases of their interest and more
• Modify the network (e.g., to keep only a specific type of relationship like activation, phosphorylation, protein-protein binding and more)
• Perform in silico prediction (e.g., if a drug, siRNA or CRISPR were to reduce the activity of a gene/protein, how will it impact the remaining genes/proteins/diseases in that network)
• Export high-resolution graphics or tabular relationships and make the created network usable in future pathway analysis

Single cell RNA-seq – data upload & analysis in Ingenuity Pathway Analysis...

Tue, 02 Apr 2024 14:53:00 GMT

This training is generated based on feedback from recent “Single Cell RNA-Seq, Cell Hashing, and Spatial Transcriptomics” training. Some registrants requested below topics to be covered in more details.
• How to upload single cell RNA-seq data in IPA and start an analysis?
• How to do above if you don’t have CLC Genomics Workbench?
• How to do above if you do have CLC Genomics Workbench?
• Tips and tricks regarding single cell RNA-seq data in IPA
• Possibly other topics based on user feedback

Multi-omics (metabolomics, proteomics, transcriptomics) analysis using...

Thu, 28 Mar 2024 14:53:00 GMT

· Generate associations among molecular signatures obtained via integrating multi-omics data

· Extract mechanisms from multi-omics data for precision medicine

· Disease stratification based on multi-omics profiles

· Map disease networks among targets and indications

Introduction to Analysis Match in IPA - Compare your gene and protein...

Wed, 14 Feb 2024 13:27:00 GMT

With all the expression datasets that are available to the public, wouldn’t it be great to compare them to your own expression data, so you could get a better understanding of the underlying biology of your data?

With QIAGEN IPA Analysis Match, you can compare your expression data with well over 100,000 publicly available datasets that have been processed and analyzed in IPA, as well as all the IPA analyses that you have performed to date.

In this webinar, we will cover how Analysis Match works and demonstrate this feature with a live demonstration. Feel free to follow along with your analysis and ask questions along the way!

IPA deeper dive: Making most out of user’s core/expression analysis and new...

Wed, 31 Jan 2024 19:17:03 GMT

Many of you who use QIAGEN Ingenuity Pathway Analysis (IPA) have requested a deeper dive into the IPA core analysis (also known as expression analysis), which is - performed on RNA-seq, scRNA-seq, proteomics and many other types of ‘omics data). You’ve specifically requested to cover topics like causal networks, regulator effects, etc., in more detail. That’s why we’ve designed this training to focus on these topics and more:
· What are the different result types of results produced by an IPA core analysis?
· What are the differences between causal network vs. mechanistic network vs. regulator effects?
· How do you predict molecular activity in IPA? What is a Z-score? · What is the new bubble plot feature?
· How can I edit, expand and modify the network the way I want it? For example, add a disease or gene(s) of interest, remove certain connections, etc?

Discovery from public data (GEO, SRA and more) using Ingenuity Pathway Analysis

Mon, 20 Nov 2023 17:52:37 GMT

Per user feedback, we are hosting a comprehensive training on how to effectively use sample level public data and metadata from sources like GEO, SRA, TCGA, GTEx, Blueprint, CCLE and other sources through Ingenuity Pathway Analysis (IPA) and IPA Analysis Match Explorer feature. The trainer will walk through usecases in realms of biomarker discovery, drug target investigation, studying survival in custom patient cohorts, multi-gene correlation and more.
Note: The word “condition” below refers to different diseases, disease subtypes, treatments, cell types, cell lines and more.
This training will cover topics like
• How is a gene of interest expressed across different conditions?
• Is there correlation in expression for two genes or biomarkers of user interest for a given condition?
• For a given condition of interest, can we derive a list of genes (example genes specific to a disease, treatment or cell type)?
• Can we generate custom cohorts of patients (example TP53 wt vs mutant or PDCD1 high vs low expression) and then generate survival curves representing those cohorts? Can we generate p-value to see if there is significant difference?
• Recent update: Can we detect expression of a gene in different cell types from single cell data?

The epididymis: Balancing the burden and responsibility of fertility

Fri, 03 Nov 2023 15:04:46 GMT

The responsibility of fertility is disproportionately placed on women, who bear most of the health, emotional and financial burdens. Infertility is rapidly rising, with one in six Australian couples seeking assisted reproductive technologies to help them start a family, and over 50% of cases involving a male factor. Despite these contributions, we still don’t fully understand the mechanisms that create competent sperm for fertilization, which occurs during their transit from the epididymis, a highly specialized region of the male reproductive tract.

To address this knowledge gap, we used high-resolution tandem mass spectrometry and in-silico analyses to characterize proteome-wide changes in mouse sperm. We studied changes associated with their transit through the epididymis and elicited in response to capacitation stimuli, such as maturation initiated upon contact with the female reproductive tract.

In this webinar, you’ll learn about:

The unprecedented depth of >6000 proteins and 14,586 site-specific phosphorylation events across these sperm populations that we discovered using QIAGEN Ingenuity Pathway Analysis (IPA)
How sperm shed over 56% of their proteins during this process, producing a refined fertilization-competent cell
How this reduced proteomic complexity of sperm coincides with the activation of certain functions, such as sperm motility and capacitation
Key proteins and kinases we identified through selective pharmacological inhibition that regulate sperm function
The role of RHOA on mature spermatozoa to reduce the rate of acrosome reaction by about 40%
Our data represent an essential paradigm shift in our understanding of male fertility regulation. They will contribute to important advancements in developing non-hormonal male contraceptives and robust sperm selection biomarkers for infertile men.

What’s new in QIAGEN IPA Fall Release 2023?

Fri, 27 Oct 2023 13:52:44 GMT

Interested in learning about new features and functionalities that have been added to IPA lately?
During this webinar, we will highlight the updates from the QIAGEN IPA Fall Release and from previous releases from this year. Topics, amongst others, will be
• Newly added findings and pathways
• Reactome pathways
• Artificial intelligence approves to pathways
• More precise matches in Analysis Match
• Cell type prediction
• New queueing view for checking your analysis status

Multi-omics (metabolomics, proteomics, transcriptomics) analysis using QIAGEN...

Wed, 25 Oct 2023 18:44:25 GMT

· Generate associations among molecular signatures obtained via integrating multi-omics data

· Extract mechanisms from multi-omics data for precision medicine

· Disease stratification based on multi-omics profiles

· Map disease networks among targets and indications

Introduction to Phosphorylation Analyses in QIAGEN Ingenuity Pathway...

Thu, 05 Oct 2023 13:28:52 GMT

In this training, we’ll introduce how you can analyze and interpret your phosphoproteomics data in QIAGEN IPA. Using an example phosphoproteomics dataset, we will answer questions such as:
• How can I format the data before uploading it into QIAGEN IPA?
• How do I set up the analysis?
• Which upstream kinases are implicated in the observed phosphoproteomics changes?
• What are the targets of a particular upstream kinase and how do their levels of phosphorylation change over time?
• How do the levels of phosphorylation change for proteins on Canonical Pathways over time?
• Which biological predictions trend in a time-dependent manner during the time course?
• How do the biological predictions from phosphoproteomics compare with a related transcriptomics dataset?

Cross-species comparison and validation for drug discovery and biomarker...

Wed, 27 Sep 2023 14:11:02 GMT

Some human studies may be unfeasible or unethical, making cross-species research critical for drug discovery and biomarker validation. Cross-species research is a crucial method to collect data to examine potential toxicity for a candidate drug, determine the efficacious doses that may be suitable for humans, identify potential biomarkers for a disease of interest or a therapeutic response and understand the mechanisms of disease or treatment. While animal models and humans have similar anatomy and physiology, the subtle differences among organisms in the animal kingdom need to be considered and data collected must be interpreted using a meaningful method.

Using QIAGEN IPA, you can perform comparative analyses across various animal models, even combining different time points, treatments, tissues and cell types with data generated from a wide variety of ‘omics technologies (RNA-seq, scRNA-seq, proteomics, metabolomics, etc.). In this training, you will learn how to:
1. Generate activity heatmaps and expression charts comparing different pathways and regulatory networks across different species
2. Use Activity Plot, Pattern Search and Analysis Match to compare your own data against thousands of public data pre-curated and pre-analyzed representing an array of disease states, conditions and other biological conditions
3. Create expression and correlation plots using pre-curated and pre-analyzed public data to validate and confirm findings derived from a comparison analysis

Analysis of exposure to perfluoroalkyl and polyfluoroalkyl substances (PFAS)...

Fri, 22 Sep 2023 16:53:09 GMT

Environmental contamination of perfluoroalkyl and polyfluoroalkyl substances (PFAS) is of significant concern due to a wide range of adverse health effects induced by these chemicals, including hepatotoxicity. Analyzing next-generation sequencing data (NGS) from RNA-seq experiments to identify PFAS-induced adverse outcome pathways in the liver may help better understand the mechanisms of PFAS-induced hepatotoxicity. This training will use QIAGEN CLC Genomics Workbench to generate differential expression data from RNA-seq and QIAGEN IPA to study the data within a biological context and uncover molecular mechanisms and regulatory molecules.

In this training, you’ll learn how to:
• Import NGS data into QIAGEN CLC Genomics Workbench
• Generate differential expression data using template workflows
• Export data to IPA
• Investigate pathways and regulatory networks to understand biological mechanisms
• Compare different experimental groups to identify biological similarities and differences
• Generate a custom network

QIAGEN Ingenuity Pathway Analysis (IPA) for grant writing and publications...

Thu, 14 Sep 2023 19:24:15 GMT

QIAGEN Ingenuity Pathway Analysis (IPA) represents a robust resource to aid in the process of writing grants publications. Driven by a wealth of manually-curated molecular interactions and associations in the QIAGEN Knowledge Base together with pre-analyzed public ‘omics data for hundreds of thousands of samples from QIAGEN OmicSoft Lands, IPA provides biological insights regardless of whether you have your own data or not. In the absence of your own data, IPA provides a resource to query existing molecular knowledge from the literature or public ‘omics data, build networks in silico, and review results from pre-analyzed public studies. With data, you can dig deeply into the biological meaning of your results through the identification of key pathways, regulatory molecules and functional changes as well as understand how your study relates to other published studies.

Join us for a 120-min training session where you will learn:

• Ways to query IPA’s vast collection of curated literature and ‘omics data
• How molecules relate to phenotypes and functions
• Build your own networks and predict activity changes
• Ways to explore a library of over 100,000 precomputed IPA analyses pulled from public ‘omics data
• How to format your dataset and set up an analysis
• How to deeply interrogate key Canonical Pathway
• How to predict regulators which are causing your expression changes
• How to contextualize the result of your analysis by comparing your results to internal and public data
• Ways to generate the necessary tables and figures for your manuscript

Compare and contextualize your results using QIAGEN Ingenuity Pathway Analysis

Wed, 23 Aug 2023 16:04:12 GMT

Take your QIAGEN Ingenuity Pathway Analysis (IPA) analyses to the next level by comparing them to your own analyses (different time points, treatments, cell lines, diseases and more) or to a library of over 100K precomputed datasets to find similar or opposite biological signatures. Identify key genes or entities and then explore how they are expressed across normal tissues, diseases and more from over 600K biological samples to gain deep context.

In this training, you'll learn how to:

• Get advanced insights with the QIAGEN IPA Analysis Match comparison feature to compare large numbers of your own datasets and/or public datasets (from GEO, SRA, cancer collections and more)
• Use and interpret the IPA Activity Plot feature to identify key genes and regulators common across datasets
• Explore identified key genes in Land Explorer to query and visualize expression across tissues, disease states and mutation status, including survival curves

We will feature these specific IPA analyses:
• Analysis Match, Activity Plot and Pattern Search
• Land Explorer
• Summer 2023 update and more

Part II: Single-cell RNA sequencing data interpretation using QIAGEN...

Mon, 21 Aug 2023 20:05:53 GMT

This two-part series will walk you through single-cell RNA sequencing (scRNA-seq) analysis starting with a matrix file or FASTQ files and ending with a deep understanding of key pathways, regulators and cell type signatures within your data.

In this session, we'll explore how you can take your scRNA-seq differential expression results produced from QIAGEN CLC Genomics Workbench (or from another software/package) and upload them into QIAGEN Ingenuity Pathway Analysis (IPA) to uncover a deep understanding of the biology in your experiment by exploring enrichment and activity prediction for pathways, regulators and more.

Specifically, you'll learn how to:
• Import data using the QIAGEN IPA plugin from QIAGEN CLC or data generated from a different software/pipeline/package
• Explore canonical pathway enrichment and predicted activity for your comparisons
• Find key regulators that may be responsible for the biology in your experiment
• Compare multiple core analyses and see side-by-side results for various cell types, clusters and more
• Compare the expression patterns for pathways and regulators in your dataset with over 135,000 precomputed public analyses in IPA
• Compare your complete analysis signature with over 135,000 precomputed public analyses in IPA

Part I focuses on the secondary analysis of scRNA-seq data using QIAGEN CLC Genomics Workbench. You'll learn to explore differential expression, UMAP, dot plot and more. Click here to watch Part I: https://tv.qiagenbioinformatics.com/video/87882199/part-i-single-cell-rna-sequencing