ncibtep@nih.gov

Bioinformatics Training and Education Program

Qiagen IPA Pathway Analysis Online Webinars and Training in August

These trainings are offered by Qiagen, not BTEP, and are listed here for your convenience.
(Last updated Aug.2,2024)

  • Aug. 6 @ 1 PM, QIAGEN Ingenuity Pathway Analysis (IPA) new user training

Register

Are you new to QIAGEN 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 how 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 Do you 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/products-overview/discovery-insights-portfolio/analysis-and-visualization/qiagen-ipa/
 
 
  • Aug. 8 @ 1 PM, Sharing your analysis results with others in Ingenuity

Register

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)

 

  • Aug. 13 @ 1 PM, Drug MOA and disease pathology investigation using QIAGEN Biomedical KB-HD

Register

Many research groups worldwide are investing significant time and resources in studying drug mechanism of action (MOA) and its impact on disease pathology. One critical challenge they encounter is access to a centralized source that contains high-quality, manually curated literature knowledge. To meet this need, we launched QIAGEN Biomedical KB-HD, the expert-curated database backing QIAGEN Ingenuity Pathway Analysis (IPA), to enable the scientific community and help accelerate drug discovery.
 
You will learn to use Biomedical KB-HD to:
 
• Easily pull up relevant literature findings for a drug of interest
 
• Generate a novel mechanism of action (MOA) for this drug and its effect on the disease indication of interest
 
• Identify new applications for this drug (drug repurposing)
 
• Investigate mutational impact on drug MOA
 
 
  • Aug. 15 @ 1 PM, Leveraging high-quality public proteomics data for biomarker and drug target investigation through OmicSoft Lands APIs

Register

Per feedback from recent trainings, we are hosting a training focused on biomarkers and drug target investigation through effectively utilizing high quality curated public proteomics expression data. OmicSoft Lands database is a high-quality curated repository containing gene and protein expression data derived from a variety of sources such as CPTAC, TCGA, HPA, GTEx and more.

Using OmicSoft Lands APIs, you will learn how to:

• Easily locate proteomics samples and projects (studies) of interest (example can we locate proteomics data related to the breast cancer or specific drug treatment?)

• Check expression of a protein of interest (drug target or biomarkers) across different experimental groups or conditions (diseases, treatments, cell types and more) as well as across samples coming from different collections (example is a protein upregulated in breast cancer samples from TCGA and CPTAC but downregulated in normal samples from TCGA, GTEx and HPA)

• Correlate protein levels with RNA-seq expression data for the same samples, and compare differential expression results from proteomic and RNA-seq results

• Investigate whether there is correlation in expression between two (or a group/list of proteins) across different experimental groups/conditions (example do two proteins of interest show correlation in expression in TNBC samples? Is protein and gene expression correlated as well?)

• Derive a protein signature from conditions of interest (example are a group of protein upregulated in disease condition but downregulated upon drug treatment)

• Perform Geneset Enrichment for a group of proteins

 

  • Aug. 20 @ 1 PM,  Single Cell RNA-Seq, Cell Hashing, and Spatial Transcriptomics

Register

A slide illustrating some of the many result types/graphics you will be able to generate after this training. https://qiagen.showpad.com/share/jYTCDPNfz1SdIMPQPSPYS

Description: In this training, you will learn how to analyze and interpret your own single cell RNA-seq data using QIAGEN CLC Genomics Workbench starting with either FASTQ or matrix files.

Using CLC Genomics Workbench, you will learn how to perform secondary analysis on your single cell RNA-seq data. Specifically, you will learn how to:

• Import your raw FASTQ or processed cell-matrix files.

• Use pre-configured but customizable pipelines/workflows for single cell RNA-seq data.

• Generate high resolution visuals and other files from your analysis for publications and biopharmaceutical discoveries.

o Dimension reduction (UMAP, t-SNE) plots

o Differential expression table for clusters, cell types, or combination of both

o Heat map o Dot plots o Violin plots

• Learn how to use “Create Cell Annotations from Hashtags” for cell hashing (i.e., CITE-seq).

• Dive into spatial transcriptomic analysis, the latest feature in the single cell RNA-seq module.

 

  • Aug. 27 @ 1 PM, IPA deep dive: miRNA investigation using QIAGEN Ingenuity Pathway Analysis (IPA)

Register

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