tv.qiagenbioinformatics.com

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 re...

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...

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 ana...

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

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

There is an almost incomprehensible amount of diverse, non-standardized ‘omics data deposited in different public sources such as GEO, SRA, TCGA, GTEx and others. Scientists who are interested in biomarker discovery and investigation using such data run into the challenge of finding time and resources to locate studies of their interest and then making it usable by cleaning and standardizing these data. Accordingly, this training is focused on how scientists facing the above challenges can use OmicSoft Lands which has manually curated, unified data which is flexibly accessed through both a web-based portal and APIs.

• Easily and...

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 th...

This hands-on workshop will cover a highly requested use case using OmicSoft Explorer and IPA Interpret, two new features that QIAGEN IPA* and OmicSoft customers can now access.

Specifically, the trainer will go over how to:

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

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

• Study volcano plots to identify biomarkers associated with conditions of int...

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

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 relat...

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 fo...

In this webinar, the speaker will cover how to simplify your single cell RNA-seq analysis with biologist-friendly point and click tools.

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

• Generate dimension reduction (UMAP, t-SNE) plots to understand differences between cell clusters/experimental conditions

• Identify and study clusters and cell types specific biomarkers using differential expression tables, gene expression heat maps, dot plots and violin plots

• Generate desired cell annotations using hashtags

• Visualize and investigate spatial transcriptomics plot using your Cell Ranger output to better...

Precision medicine is rapidly transforming healthcare, and one of the most significant accelerators of its progress has been the dramatic reduction in cost. In this webinar, we explore how innovations in genomics and biotherapeutics are making advanced, personalized healthcare more accessible and affordable than ever before. Dr. George M. Church will examine how the cost of whole genome sequencing has been reduced from $3 billion per haploid genome—previously unusable in clinical settings—to just $300 per phased diploid genome today. We’ll also look at the economics behind cell therapy, such as blood transfusions (now as low as $200), and gene t...

The 37 trillion cells of the human body have a remarkable array of specialized functions and must cooperate in time and space to construct a functioning human.

In this webinar, Sarah Teichmann, professor of stem cell medicine at the University of Cambridge and co-founder and co-leader of the International Human Cell Atlas Consortium, discusses how her lab harnesses cutting-edge single-cell and spatial genomics to better understand this cellular diversity — specifically, how distinct microenvironments regulate cell identity.

The lab’s spatial atlas of the adult human heart includes the first comprehensive map of the conduction system, and...

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

Bu...

Cancer care has been transformed by comprehensive molecular profiling and targeted therapies – but with improvements in sample analysis technologies, the volume of information and burden of interpretation has exploded. Physicians need guidance from the laboratories to translate molecular results into clear treatment paths. And with the pace of innovation only accelerating, the gap between discovery and actionable insight is widening fast. Laboratories need resources to help them to manage the information and communicate it to physicians in a reliable and efficient manner.

That’s why leading labs are turning to QCI Precision Insights (formerly N-of-One), a profe...

Pathways and knowledge graphs have provided valuable insights into disease pathology, toxicology, target safety assessment, drug MOA and biological mechanisms in general. Though this is not possible without a high quality, reliable database. QIAGEN Knowledgebase is a comprehensive database with causal reasoning that is regularly updated from trusted peer-review publications and other sources using both high quality manual curation and utilizing AI/ML approaches.

In this webinar the trainer will

Introduce the QIAGEN Knowledgebase

Demonstrate how the user can take advantage of an easy-to-use graphical interface to study pathways and networks of...

The Cancer Gene Census (CGC) is a widely used module within the Catalogue Of Somatic Mutations In Cancer (COSMIC) that comprises an ongoing effort to catalogue and describe all genes with causal impact in human cancer. In CGC, genes are characterized according to their roles in cancer – tumor suppressor, oncogene or fusion gene – and divided into two tiers based on the strength of supporting evidence. On

October 15, our COSMIC and QIAGEN field applications experts will walk you through the scientific and curation processes behind CGC. We will also explore another module, the Cancer Mutation Census...

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.

Dimension...

QIAGEN CLC Microbial Genomics Module provides tools and workflows for a broad range of bioinformatics applications, including microbiome analysis, isolate characterization, functional metagenomics and antimicrobial resistance characterization. The module supports the analysis of bacterial, viral and eukaryotic (fungal) genomes and metagenomes.

This training will be focused on amplicon-based taxonomic profiling (16S/18S/ITS sequencing OTU clustering). The trainer will cover:

Overview of different tools within QIAGEN CLC Microbial Genomics Module and supported research areas

For taxonomic profiling:

Importing data 

Utilization of metadata 

Downloading and managing references 

QIAGEN OmicSoft Lands are high-quality curated repositories of genomics and proteomics data sourced from public, published studies (GEO, EBI, SRA) and consortia (TCGA, CPTAC, GTEx, and more). Because of our expert curation and stringent quality checks, OmicSoft users can deeply investigate across diverse oncology and normal tissue/cell datasets to discover and validate candidate drug targets and biomarkers.

In this training, attendees will use OmicSoft Studio, our graphical user interface, to access public data from The Cancer Genome Atlas (TCGA). Using this data, you will learn how to:

• View gene expression and somatic mutation fr...

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...

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 fo...

See how highly sensitive somatic detection of classic tumor reference samples is made possible through the Twist Oncology - DNA CGP Panel™ combined with downstream analysis using QIAGEN® CLC Genomics Workbench.

What is the Twist Oncology - DNA CGP Panel?

It is a panel from Twist Biosciences® that is designed for the comprehensive genomic profiling (CGP) of solid tumors to find pathogenic variants. It also supports the scoring of microsatellite instability (MSI) and tumor mutational burden (TMB).

What is QIAGEN CLC Genomics Workbench?

A powerful all-in-one analy...

In this video we introduce sample batching using CLC tools. This can be helpful when you need to perform the same analysis on a large number of files. Also see this manual page  for more details:

https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Batch_processing.html

This video demonstrates how to analyze multiple input files per sample using batch mode. Please also see this FAQ page for more details:

How can I run a batch job with multiple libraries for each sample?   

The history view keeps track of what tools and parameters were used to generate results in CLC. This video shows how the history view can be used to compare two different analyses when the results are unexpected.

Details about the history view can be found on this manual page:

https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=History_Element_Info_views.html

This video provides a quick introduction to myCLC. If you do not already have access to myCLC Please contact bioinformaticslicense@qiagen.com

Also, check out these FAQ pages:

What is myCLC?  

How can I get access to myCLC?  

How can I find information about my CLC licenses?   

How can I add someone as a technical contact to myCLC?  

How can I view information for another myCLC account?

In this video you can learn how to import tracks and create a track list in CLC. Track lists enable users to view multiple track elements at once. Track lists also feature an interactive link between the table view and the plot view.

Use track lists to browse genomic features, zoom into regions of interest, visualize read mappings, inspect variants, and more. Please also see this manual page for more details:

https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Track_lists.html

This video shows how to customize volcano plots in CLC Genomics Workbench. Check out these tutorials for more RNA-seq related topics:

https://digitalinsights.qiagen.com/support/tutorials/#:~:text=Expression%20and%20fusions

More and more biopharma and academic groups are looking to process a large number of samples simultaneously or for a quicker turnaround time. This webinar will introduce a flexible and powerful setup for running your NGS sequence analyses through servers or Amazon Web Services (AWS). See how QIAGEN CLC Genomics Workbench can be used to customize workflows and send analyses for batch execution. We will also highlight analysis automation solutions, use of third-party dockers, audit trails and user management – all of which are available within the CLC Genomics Server software.

You will learn to:

• Cust...

The increasing adoption of next-generation sequencing in many fields has made RNA-seq data analysis and interpretation essential skills for researchers. In this webinar, discover how you can effortlessly process FASTQ files with QIAGEN CLC Genomics Workbench (CLC). Next, you will import differential expression results directly into QIAGEN Ingenuity Pathway Analysis (IPA) for downstream analysis – enabling a smooth path from data to discovery.

You will learn how to:

• Use CLC to map reads to a reference genome, generate gene/transcript counts and QC reports

• Use CLC to visualize results, such as heatmap...

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, ta...

Join us for an in-depth webinar showcasing the discovery of functional insights in microbial communities using QIAGEN CLC Genomics Workbench tools. Ideal for microbiologists, bioinformaticians and researchers aiming to uncover functional signatures in microbial communities and drive data-driven discoveries, you will learn how to perform a comprehensive whole metagenome functional analysis, from raw NGS data to functional profiling and visualization.

Whether you are working with experimental or clinical samples, this session will equip you with a robust, scalable pipeline for comparative functional metagenomics.

Learn how to:

• Import and prep...

From clinicians to translational researchers to drug developers, everyone is feeling the pressure to match patients with the right therapy faster. The challenge intensifies with rare and inherited diseases, where information is limited and affected individuals are few and scattered across the world.

But you can cut weeks from your variant interpretation workflow – without compromising accuracy. On September 24, see how Human Gene Mutation Database (HGMD) Professional can shorten the path to germline variant insights using expert-curated data. Explore almost 30 years of curated variant knowledge, spanning over 17,600 genes and more than 38,000 phenotypes.

Le...

QIAGEN CLC Genomics Workbench allows easy construction and customization of variety of bioinformatic analysis workflows such as DNA-seq, RNA-seq, De Novo Assembly and more. Per feedback received, this session will focus on

• A quick and brief introduction to CLC Genomics Workbench

• How to construct a workflow

• How to add or remove different steps

• How to customize different parameters

• How to execute the workflow

• (Optional) How to install the workflow

Join us for a focused webinar showcasing the Type Influenza Strain workflow within QIAGEN CLC Genomics Workbench. This streamlined, template-based workflow enables efficient typing of targeted Influenza virus sequencing data by integrating consensus sequence refinement, reference-based subtype identification and mixed-infection variant detection.

We’ll show how the workflow:

Automatically determines Influenza virus type and subtype

Outputs annotated consensus sequences with gene and CDS tracks for intuitive visualization

Detects low-frequency variants that may indicate mixed infections

Presents results in a consolidated, interactive track list in both...

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

• Build your own network...

This webinar will focus on running the fusion detection analysis within QIAGEN CLC Genomics Workbench and annotating the detected fusions using curated clinical knowledge from Human Somatic Mutation Database (HSMD). Finally, the data will be uploaded to QIAGEN Clinical Insight (QCI) applications for further analysis.

You will learn:

• How fusion detection algorithms work

• To run the fusion detection template workflow

• To interpret the analysis results

• To annotate fusions with HSMD

• To upload and analyze the fusions with QCI Interpret

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

Join us for an in-depth walkthrough of HPV integration site mapping using the CLC Microbial Genomics Module. This webinar presents a rapid, automated workflow for identifying and visualizing viral integration sites (VIS) in the human genome, using data from HPV-positive cervical samples. By leveraging the Viral Hybrid Capture (VHC) and VIS Identification workflows, researchers can perform end-to-end analysis—from taxonomic profiling to pinpointing virus-host breakpoints. Learn how this streamlined pipeline enables high-resolution visualization, accurate integration mapping, and efficient reporting to advance our understanding of HPV-driven carcinogenesis.

Key Takeaways:

• End-to-End Automation: Explore how the CLC Geno...

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

In this 90-minute video, users will learn how to discover and validate biomarkers, key regulators and targets through harnessing uniformly-processed public data from sources such as GEO, SRA, cancer collections (TCGA, CCLE etc.), normal tissue/cell type collections (GTEx, HPA etc.) and more using QIAGEN Omicsoft Lands.

Single-cell gene expression analysis helps biologists and bioinformaticians reveal complex and rare cell populations, uncover regulatory relationships among genes and analyze and visualize gene expression differences among different cell types, or within a unique cell type. In this talk we will explore new tools for analyzing, interpreting and explore scRNA-seq data and the underlying biology. We will also show how to integrate ‘omics datasets from different platforms to gain insights into the biology and molecular drivers of specific cell populations.
Objectives:
How to analyze scRNA-seq data without a bioinformatician or learning code.
How to leverage automatic ce...

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...

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...

In this training, users will learn how to generate downstream outputs such as heatmaps, differential expression tables, PCA/PCOA plots, box plots and other visualizations from their count or expression data (transcriptomics, proteomics, metabolomics, etc.). Attendees will learn how to: • Import either normalized or raw count data (transcriptomics, proteomics, metabolomics, etc.) into QIAGEN OmicSoft Studio • Generate downstream outputs such as differential expression tables, heatmaps, counts, PCA/PCOA, etc. • Export high resolution graphics as well as raw or filtered tables • Export results to QIAGEN Ingenuity Pathway Analysis • Deploy easy-to-use pipelines for RNA-seq/scRNA-seq/microarray data • Implement options for downloading or comparing pu...

In this 90-minute training, users will learn how to do drug treatment, toxicology and target safety assessment related discoveries using QIAGEN Ingenuity Pathway Analysis (IPA) and QIAGEN Omicsoft Lands.

Using public data from GTEx (normal tissue), GEO, cancer collections and more, attendees will learn how to use Omicsoft Lands to:
• Investigate a drug target or biomarker expression across different normal tissues, disease conditions, treatments and more
• Correlate expression of 2 or more genes
• Identify a list of genes or biomarkers specific to treatment, disease, normal tissue, cell type and more

Using findings from p...

In this 90-minute training, attendees will learn how to use basic expression analysis functionalities in QIAGEN OmicSoft OncoLand. QIAGEN OmicSoft Single Cell Land will also be discussed, focusing on public single-cell data.

Key focus will be on Biomarker discovery with QIAGEN OmicSoft OncoLand leveraging public oncology data from GEO, TCGA and other collections to:

• Discover and validate biomarker expression in diseases, disease subtypes, treatments, cell types, etc.
• Identify a list of biomarkers specifically expressed in disease, treatment group, cell type or other condition of interest
• Overlay expression of a gene on cell clusters of intere...

This training will focus on how QIAGEN Omicsoft Studio and IPA can be used to discover new biomarkers, validate (or study) drug targets and identify novel mechanisms of action with user and/or public checkpoint inhibitor datasets from resources like GEO, SRA, TCGA and more.

In this training, you will learn how to:
· Investigate the expression of a gene/biomarker/drug target across different treatments and diseases
· Derive a biomarker/gene signature from a specific condition (for example, non-responders of a drug, a specific disease/disease subtype and more)
· Correlate expression of multiple genes and...

Slides from this training:
https://qiagen.showpad.com/share/qm9IZA718x6x5h6pfsiTa

Single cell lands tutorials: https://omicsoftdocs.github.io/ArraySuiteDoc/tutorials/SingleCellLand/Gene_Views/

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

In this training, attendees will learn how to

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

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

In this training, attendees will learn how to

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

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

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

· Identify key...

Have you ever tried to access the genomic profiles of cell lines before using them in your preclinical experiments just to come up empty-handed? Maybe you’ve scoured public databases for gene expression information on your cell line to find the reported genomic profile doesn't match the cell line data you recently purchased?

We understand that knowing the genomic identity of your cell lines is fundamental to the success of your preclinical experiments. Unfortunately, most publicly available sources have little or no cell line' omics data, leaving you to fend for yourself.

That's why we've teamed up...

In this 90-minute training, you’ll learn how to do drug treatment, toxicology and target safety assessment-related discoveries using QIAGEN Ingenuity Pathway Analysis (IPA) and QIAGEN Omicsoft Lands.
Using public data from GTEx (normal tissue), GEO, cancer collections and more, you’ll learn how to use Omicsoft Lands to:
• Investigate a drug target or biomarker expression across different normal tissues, disease conditions, treatments and more
• Correlate expression of two or more genes
• Identify a list of genes or biomarkers specific to treatment, disease, normal tissue, cell type and more

Using findings from peer-reviewed publications and other...

In the rapidly evolving landscape of drug discovery, the ability to integrate high-quality research findings into knowledge graphs is paramount. For over twenty years, our scientists have curated the relationships between genes, drugs, diseases, and pathways to power Ingenuity Pathway Analysis. Now, these data are available via our QIAGEN Biomedical KB-HD, which provides direct access to flat files, SQL APIs in Python and R, and the ability to export knowledge graph objects for analysis in Neo4j.

In this talk, we will explore how to use this rich data resource to:

• Aggregate relevant findings ac...

Since the completion of the Human Genome Project over two decades ago, genomics has become progressively entrenched within the bedrock of the biomedical research enterprise. Capitalizing on the momentum of the project’s successful completion, the field of genomics has increasingly expanded and matured, such that genomics is now central and catalytic in basic and translational research, and studies now regularly demonstrate the vital role that genomic information can play in clinical care.

Looking ahead, the anticipated advances in technologies, biological insights, and clinical applications (among others) will lead to more widespread dissemination of genomics throughout bi...

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...

 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 recen...

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

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.

There is an almost incomprehensible amount of diverse, non-standardized ‘omics data deposited in different public sources such as GEO, SRA, TCGA, GTEx and others. Scientists who are interested in biomarker discovery and investigation using such data run into the challenge of finding time and resources to locate studies of their interest and then making it usable by cleaning and standardizing these data. Accordingly, this training is focused on how scientists facing the above challenges can use OmicSoft Lands which has manually curated, unified data which is flexibly accessed through both a web-based portal and APIs.

• Easily and...

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.

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 fo...

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-direct...

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 an...

For your RNA-seq data, you will learn how to:

• Import FASTQ files, cell matrix files and metadata

• Download and/or import reference and annotations files

• Map reads to a reference genome

• Generate gene and transcript counts

• QC reports displaying % mapped reads etc.

• Generate visualizations of results, such as heatmaps, differential expression tables, PCA/PCOA plots, Venn diagrams, Sankey plot and more

• Easily customize RNA-seq workflows

• Export publication-quality graphics, tables and reports

Per audience request

• Send differential expression tables to QIAGEN Ingenuit...

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.

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 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.

Learn how to add users to your QIAGEN Digital Insights (QDI) license through the QDI Admin Tool (QDIAT).

The gene therapy space continues to grow with the discovery of new gene editing targets. Meanwhile, new indications are being identified for known targets by exploring vector biology and the biological mechanisms underlying disease pathology.

In this webinar, we will show how Biomedical KB-AI accelerates target discovery and indication expansion using generative AI. Biomedical KB-AI provides a more comprehensive view of the biological landscape, enabling the identification of novel relationships and patterns that may be missed by traditional methods.

You will learn:

• About Biomedical KB-AI and its structure

• How to easi...

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 fo...

As the adoption of relational and deeply curated ‘omics databases increases, creating SQL queries has become a mandatory skill rather than a desirable one. Through this training, we will equip you with the know-how and best practices around designing SQL queries – no prior SQL experience required. And while we will use QIAGEN biomedical databases, the knowledge you acquire can be easily applied to other databases.

Topics will include:

• Some basics of SQL

• A brief introduction to databases being used

• How to generate queries that can help you answer scientific questions (related to...

S2I oncology

 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 2: Formatting and Uploading Your Dataset into IPA

Learn how to format your own data and upload it into IPA...