tv.qiagenbioinformatics.com

Novel discoveries from public single-cell RNA-seq data using QIAGEN OmicSoft...

Mon, 25 Aug 2025 10:44:24 GMT

QIAGEN OmicSoft Lands and QIAGEN Ingenuity Pathway Analysis (IPA) provide a powerful resource for exploring curated pre-analyzed public single-cell RNA-seq studies and providing downstream biological insights for these data. In this training, we will review how OmicSoft Lands allows for the interrogation of identified cell types within public single-cell datasets of interest and subsequent exploration of their associated gene signatures. The biological context of these signatures can then be explored within QIAGEN IPA, identifying key pathways and their associated activity, as well as predicting regulatory molecules that could function as biomarkers or drug targets. In addition, the biological signatures found in relevant cell types can be evaluated through comparison with other pre-analyzed single-cell and bulk RNA-seq studies to explore the conservation of these biological signals.

In this webinar you will learn how to:
• Easily search and locate scRNA-seq projects of interest within QIAGEN OmicSoft Lands
• Determine gene expression signatures associated with cell types of interest
• Easily search and interpret pathway analyses of pre-analyzed single-cell studies within QIAGEN IPA
• Quickly identify and interpret key biological pathways and regulatory networks within QIAGEN IPA
• Compare the biological findings for a cell type to other single-cell and bulk gene expression studies
• Export results in graphical and tabular formats of interest

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.

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.

Data Formatting in IPA

Thu, 10 Jul 2025 16:24:35 GMT

Learn how to format your dataset for upload and subsequent analysis in IPA. In this video tutorial, you will discover the best practices for structuring your dataset and the data measurement value types you can use for various IPA analyses.

Interested in learning more?

Click here

IPA data upload tutorial

Tue, 01 Jul 2025 11:48:00 GMT

Presented by Lynne Mullen, Ph. D.

IPA data formatting tutorial

Tue, 01 Jul 2025 11:47:04 GMT

Presented by Lynne Mullen, Ph.D.

Part II: Formatting and Uploading your Data into IPA

Tue, 01 Jul 2025 11:37:04 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 to perform the many different types of analyses offered in IPA. In this webinar we will use phosphoproteomics data as an example dataset.

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

Understanding the P-Value of Overlap Statistic in IPA

Fri, 27 Jun 2025 21:28:20 GMT

Learn how to interpret your p-value of overlaps results in IPA. You can gain a deeper understanding of the right-tailed Fisher’s Exact Test, why it’s used in IPA, how the results are calculated, and caveats to keep in mind when interpreting your results.
For more information visit our website

Sections:

0:00-1:09 Introduction to the video. The two types of p-values that are relevant for IPA and how they differ.

1:09-2:25 History of the Fisher’s Exact Test: the “Lady Tasting Tea” experiment.

2:25-5:50 Hypothesis testing for enrichment in IPA. The reference set, the null hypothesis used, and the overlap of molecules defined.

5:51-7:58 Why the right-tailed Fisher’s Exact Test is used in IPA.

7:58- 8:41 Explanation of sampling and expected proportions from the hypergeometric distribution.

8:41-9:34 Defining significance levels in the distribution. Why only the right-tailed, rather than two-tailed test, is considered in IPA.

9:35-11:04 The p-value defined and default significance level used in IPA.

11:04-11:12 How the p-value is calculated. How data is entered into the 2 x 2 contingency table and the formula used.

11:13-13:34 Example calculation and interpretation using the “Lady Tasting Tea” experimental data. Why the p-value of overlap calculations are Exact.

13:35-15:09 Transcriptomics example: Number of molecules tested and how they are categorized.

15:10-16:10 Transcriptomics example: data in 2 x2 contingency table, p-value calculation performed and interpreted.

16:11-18:07 Caveats for using and interpreting the p-value of overlap statistic in IPA.

18:08-18:36 Where to find more information about IPA and Customer Support information.

Easily process your FASTQ files

Fri, 17 Nov 2023 13:47:09 GMT

Do you ever get stuck processing raw FASTQ data or cell matrix data from your RNA-seq, scRNA-seq or other NGS assays using? Are you interested in creating a differential expression table that’s compatible with the QIAGEN Ingenuity Pathway Analysis (IPA) software you use? In this training, you’ll learn how to use QIAGEN CLC Genomics Workbench to easily process your FASTQ files and generate differential expression tables without using command line tools. We’ll also explore how you can generate other desired outputs, such as volcano plots, heatmaps, PCA/PCOA plots and more.

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

Proteomics and phosphoproteomics data interpretation using QIAGEN Ingenuity...

Tue, 02 May 2023 09:21:28 GMT

In this QIAGEN IPA training, we’ll focus on interpreting proteomics and phosphoproteomics datasets.

In this tutorial, we’ll guide you through steps and workflows to address your questions related to interpreting proteomics and phosphoproteomics datasets using QIAGEN IPA, such as:
• How should I format the data before uploading to 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 the time course?
• What are the targets on a particular Canonical Pathway and how do their levels of phosphorylation change 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?

IPA Deeper Dive: Discoveries from comparative analyses in IPA

Tue, 31 Jan 2023 18:48:25 GMT

Take your IPA analysis results to the next level by comparing them to your own analyses or from a library of over 100k 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 600k biological samples to gain deep context.

Attendees will learn how to:

• 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)

• 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, mutation status, including survival curves

Specific IPA analyses to be featured include:

• Analysis Match

• Activity Plot

• Pattern Search

• QIAGEN OmicSoft Land Explorer

• Graphical Summary of analysis results

• Among others