Become a UseR: A brief tour of R

3/12/2021 10am PDT/1pm EDT

• Why should one use/learn R?
• How to install R/Rstudio
• Learn about R basics: variables, programming, functions
• Learn about the R package ecosystem that extends its capabilities
• See a basic statistical analysis example
• Learn about additional resources

From GWAS to gene: what are the essential analyses and how do we bring them together using heterogeneous stock rats?

2/26/21 10am PDT/1pm EDT

• explain the HS rat population and their history
• describe the automated pipeline that performs GWAS in HS rats
• explore the fine mapping of associated regions and explain the various secondary analyses that we use to prioritize genes within associated intervals

Beginner's guide to bulk RNA-Seq analysis

2/12/2021 10am PDT/1pm EDT

• To give a general overview of the popular Illumina technology for sequencing RNA.
• To outline several of the key aspects to consider when designing an RNA-Seq study
• To provide guidance on methods and tools for transforming reads to quantitative expression measurements.
• To describe statistical models that are typically used for differential expression and why these specialized models are needed.

• Sampled counts from every strain are now available as well as total counts.
• You can create a custom view and select total/sampled count and choos the density of the count tracks.
• Bug Fixes

• You can now create gene lists from Genome Browser tables - Filter tables from tracks, eQTLs, WGCNA based on expression/tissue and then use gene list tools on the list.
• Implemented a reasonable region restriction of 5Mbp for now. - We are working to create a less detailed view that will be displayed in larger regions.
• Bug Fixes

11/20/2020 10am PDT/1pm EDT

• Express causal inference as a missing data problem (counterfactual framework)
• Outline assumptions needed for causal inference
• Express causal information as (directed acyclic) graphs
• Outline how to use graphs to guide analytic strategy

Introduction to GeneWeaver: Integrating and analyzing heterogeneous functional genomics data 10/23/2020

• Compare a user's gene list with multiple functional genomics data sets
• Compare and contrast gene lists with data currently available and integrated in GeneWeaver
• Explore functional relationships among genes and disease across species

Using genetic and non-genetic covariates in QTL studies 10/9/2020 10am PDT/1pm EDT

• Identify covariates and mediators in QTL studies
• Adjust for covariates in QTL scans
• Review genetic relatedness in segregating populations
• Adjust for genetic relatedness using linear mixed models

Introduction to Weighted Gene Co-expression Network Analysis 9/25/2020 10am PDT/1pm EDT

• Introduction and motivation for co-expression network analysis
• Basics of weighted gene co-expression network analysis
• Step-by-step guide to WGCNA using the wgcna package in R.

Sex as a Biological Covariate in QTL Studies With Dr. Saunak Sen 9/11/2020

• Review QTL mapping
• Understand the role of sex in QTL study design
• Use sex as a covariate in QTL analysis
• Understand X chromosome segregation in crosses
• Make adjustments for X chromosome in QTL analysis

Identifying genes from QTL using RNA expression and the PhenoGen website 8/28/2020 10am PDT/1pm EDT

• Demonstrate how to use the PhenoGen website to identify transcripts:
• Physically located within a QTL
• Physically located within a QTL and expressed in brain
• With a brain cis eQTL within the QTL
• With any brain eQTL within the QTL
• Within a co-expression network controlled from the same region as the QTL

• Version 3.7.3 has been released with the following updates.
  • RNA-Seq eQTLs based on HRDP
  • Heritability based on HRDP
  • TPM summary
  • Track Table filtering
  • Table export to clipboard, csv, xls, and PDF
  • Ensembl and Reconstruction based eQTLs/TPM/Heritability

• Version 3.7.2 has been released with the following updates.
  • RNA-Seq eQTLs
    • Gene Track Summaries now include RNA-Seq based eQTL summaries
    • Modules for a region can be selected base on overlap of the module QTL with the region.
    • Genes with an eQTL that overlaps the region are now available based on RNA-Seq and Microarrays
  • Custom Views
    • Total Counts for all 45 strains to date are available.
  • Read counts for all 45 strains are available to add as browser tracks.
  • Bug Fixes

QTL to gene/molecular networks 6/12/2020 10am PDT/1pm EDT

• Define eQTL
• Examine the role of eQTL in the relationship of genes and molecular networks with phenotypic QTL
• eQTL for co-expression networks

Quantitative Genetics Tools

• Version 3.7.1 has been released with the following updates.
  • Downloads
    • Tissue Specific/Merged Reconstruction GTFs
    • Normalized Expression Values for Ensembl/Reconstruction, Gene/Transcript, Strain Means/Individual values
  • Custom Views
    • Build a custom view on the fly by selecting a few check boxes simply select sissue and track types.
    • Views can be named and saved for future use

• Version 3.7 has been released with HRDP v5.
  • Transcriptomes are now based on the full HXB/BXH RI panel in brain and liver and available inbred strains now including the F344/Stm and LE/Stm strains.
  • Updated WGCNA, expression values, eQTLs, and transcriptomes are available.
  • Transcript level expression is available for the full panel.
  • Transcript level eQTLs are now available once you've selected a gene.
  • Transcript level WGCNA is coming in the next 1-2 months.
• CircularRNA data is availble now. This includes predictions from BNLx/SHR in Brain/Heart/Liver using CIRI 2.0 and CircExplorer2. Also Heart left ventricle includes data from more than 12,000 previously described cirRNAs using cirRNA arrays. Full reports are coming soon but the browser includes tracks with annotation and structure all available data.

• Version 3.6 has been released with HRDP v4. Transcriptomes are now based on the full HXB/BXH RI panel in brain and liver and available inbred strains except for the F344/Stm and LE/Stm. The FXLE/LEXF parents will be included in HRDP v5. Updated WGCNA, expression values, eQTLs, and transcriptomes are available. Transcript level WGCNA is coming in the next 1-2 months. Transcript level expression is available again now for the full panel.
• Links to Literature searches for gene-gene/gene-keyword relationshipts and gene-Addiction relationships.
• Shortcuts to the genome browser to get you to sections of interest more directly.
• New gene list eQTL image/browser.

Look for another workshop spring/summer 2020

• Gene List tabs have been reformatted so you can submit submit new analyses and view results and running analyses status from a single page.
• GO term summaries are available for Gene Lists.
• MuliMiR results are available for Rat both in Gene Lists and the browser(individual genes, WGCNA modules).

• The UCSC Repeat Mask track is now available.
• You now have the ability to add tracks without going into the edit view option.
• We've also fixed a number of bugs and made general functionality improvements.