Bioinformatics

This class will provide a demonstration of different options for cell type classification and treatment group comparisons at different levels with multiple samples of Single Cell RNA-Seq data. A CITE-Seq data will also be used to illustrate how to integrate protein and RNA information. Attendees will also learn how to integrate histology information with gene expression profile using a Spatial transcriptome data set.

This first of five webinars will introduce NIH’s All of Us Research Program, including the program’s mission and core values. Learn about the current size and diversity of the participant cohort and the data types and tools available to researchers. Attendees will also see examples of recent research using the All of Us dataset. 

This session will outline the All of Us Researcher Workbench registration process for NIH researchers. Access to the Researcher Workbench is free, and all registered researchers are provided $300 initial computational credits. Some analyses in the cloud may incur additional costs beyond these credits. Attendees will also learn how to create a Google billing account in case they use up their initial credits. Finally, attendees will hear about funding opportunities that can support using the All of Us dataset. 

In this webinar, attendees will learn the basics of using the All of Us Researcher Workbench’s point-and-click research tools, including how to create a workspace, how to build a cohort of All of Us participants using the Cohort Builder, and more. 

Webinar attendees will hear tips and tricks to code efficiently in the Researcher Workbench using R and RStudio. Although Python and SAS are alternative programming languages available on the Researcher Workbench, this session will only focus on using R and RStudio. Participants should already have a general understanding of how to code in R prior to attending the session. This session will not cover the basics of coding in R.

Webinar attendees will learn how to use and navigate the All of Us Researcher Workbench’s User Support Hub, which provides video tutorials, help articles, and more. Attendees will also learn about opportunities to get support from the Researcher Workbench help desk and how to stay involved with the All of Us Research Program through the program’s network of partners. 

Presenters:

VSClinical is designed for researchers to efficiently process the clinical interpretation of cell variants based on Association for Molecular Pathology (AMP) and American College of Medical Genetics and Genomics (ACMG) guidelines. This class will demonstrate how VSClinical enables labs to test for both germline and somatic cell variants according to the American College of Medical Genetics (ACMG) and AMP guidelines in an automated fashion.

This class will provide a demonstration of how to identify cell types based on statistics, visualization, and canonical markers. One Peripheral blood mononuclear cells (PBMCs) sample will be used to illustrate a basic Single Cell RNA-Seq analysis pipeline.

This class will provide a demonstration of how to build a Bulk RNA-Seq data analysis pipeline using a fastq file. Partek Flow is a web-based application for the analysis of next generation sequencing (NGS) including RNA, small RNA, and DNA sequencing.  With an easy-to-use graphical interface and the ability to build custom analysis pipelines, Partek Flow enables users to carry out routine NGS data analysis using dozens of popular algorithms without writing codes or running command lines tools.

Galaxy is a scientific workflow, data integration, data analysis, and publishing platform that makes computational biology accessible to research scientists that do not have computer programming experience. This training will introduce ChIP sequencing data analysis followed by a tutorial showing ChIP-seq analysis workflow.  This workshop will be taught by NCI staff and is open to NIH and HHS staff.

Galaxy is a scientific workflow, data integration, data analysis, and publishing platform that makes computational biology accessible to research scientists that do not have computer programming experience. This workshop will cover exome sequencing data analysis, followed by tutorials showing the use of exome analysis workflow. The hands-on exercise will run on a Galaxy platform using Illumina paired-end exome sequencing data. This workshop will be taught by NCI staff and is open to NIH and HHS staff. 

The Human Gene Mutation Database (HGMD) database provides quick access to known published gene lesions responsible for human inherited disease. This session will explore how to query genes and mutations in HGMD and how to view the curated content.

This class will provide an overview of Bioconductor. We will learn how to identify Bioconductor packages that are appropriate for a project, explore package documentation, and demonstrate how to download and install R packages from Bioconductor. 

This session describes the application of the web-based interactive OmicCircos in R Shiny to construct circular plots with desired biological features. Example data from human and mouse genomes will be used to demonstrate over thirty plot functions along with the color selection, annotation, labeling, and zoom capabilities. User-guide, take-home video and sample plots from publications will be provided. No R Programming experience is required.

During this session we will introduce our services, answer basic questions, and arrange follow-up support for more complex queries.

This in-person hands-on workshop will introduce the Ingenuity Pathway Analysis (IPA), which is available to access from the NIH Library. IPA can be used identify biological relationships, mechanisms, pathways, functions, and diseases most relevant to experimental datasets.

This in-person hands-on workshop will introduce the Ingenuity Pathway Analysis (IPA) and CLC Genomics Workbench tools, which are available to access from the NIH Library. IPA can be used identify biological relationships, mechanisms, pathways, functions, and diseases most relevant to experimental datasets. CLC Biomedical Genomics Workbench supports a comprehensive set of NGS data analysis applications, including resequencing, read mapping, de novo assembly, and many RNA-Seq tools.

In this in-person session, participants will have an opportunity to discuss their own research and use of Qiagen products with Qiagen scientists.

Note on Technology

Participants are expected to bring their own laptops to this training. NIH Staff using an NIH-laptop can easily connect to the staff Wi-Fi. If participants are bringing a personal laptop, they are restricted to using the NIH Public Wi-Fi. 

This in-person workshop will show participants how to identify cell types based on statistics, visualization, and canonical markers. One Peripheral blood mononuclear cells (PBMCs) sample will be used to illustrate a basic Single Cell RNA-Seq analysis pipeline.

This class will provide an overview of Partek Flow software, followed by demonstrations of basic component management in Partek Flow.

The training will overview the current status of pathway tools, with focus on software available to NIH community.  It will discuss the biological interoperation of mutation and expression data in the context of pathways, pathway databases, and popular web-based pathway tools. The pathway software GSEA, g: Profiler, and PATHVIEW will be used to demonstrate how to run the pathway analysis of expression data against GO (Gene Ontology), KEGG (Kyoto Encyclopedia of Genes and Genomes), and MSigDB (Molecular Signatures Database).

Galaxy is a scientific workflow, data integration, data analysis, and publishing platform that makes computational biology accessible to research scientists that do not have computer programming experience. This workshop will introduce RNA-seq data analysis followed by tutorials showing the use of popular RNA-seq analysis packages and preparing participants to independently run basic RNA-Seq analysis for expression profiling. The hands-on exercises will run on the Galaxy platform using Illumina paired-end RNA-seq data.

Single nucleotide polymorphism (SNP) & Variation Suite (SVS) is an analytic tool created to empower researchers to perform complex analyses and visualizations on genomic and phenotypic data. Genome-Wide Association Studies (GWAS) continues to be an effective method for identifying disease susceptible genes in humans and other organisms.

Key Pathway Advisor (KPA) is a web application for biological pathway analysis of OMICs data. This session will demonstrate using KPA to: explore the biological meaning of data; predict key protein activity changes that could be the root cause of gene expression alterations; understand how biological pathways are impacted by data; create hypotheses about new targets, mechanisms of action, biomarkers and disease associations; and align results with current knowledge of biomarkers and drug targets. Bioinformatics experience is not required to use this tool.