Course Overview
Course Integrity
This course is compiled automatically on 2021-03-18
The course is tested and available on MacOS, Windows and Ubuntu Linux for R version 4.0.3 (2020-10-10)
Overview
This course introduces Genomic Variant Analysis in Bioconductor.
The course consists of 3 sessions. This walk you through each step of a genomic variant analysis workflow. It covers manipulation VCF files, annotate variants, and more advanced analysis of large cohort. Exercises and answer sheets are included after all subsections to practice techniques and provide future reference examples.
Course material and exercises are available to view as rendered HTML at https://rockefelleruniversity.github.io/RU_GenomicVariants/. All material is available to download under GPL v2 license.
Setting up
System Requirements
Install R
R can be installed from the R-project website.
The R website can be found here http://www.r-project.org/.
The download links and associated installation instructions for multiple platforms can be found below provided by Revolution Analytics. https://cran.revolutionanalytics.com
We recommend installing R 4.0.3 as this is the version used to compile the course. Direct downloads for R 4.0.3 for the main platforms can be found below:
Install RStudio
RStudio can be installed from the RStudio website.
RStudio can be downloaded for all platforms at the link below
https://rstudio.com/products/rstudio/download/
Install required packages
From the course package
install.packages('BiocManager')
BiocManager::install('RockefellerUniversity/RU_GenomicVariants',subdir='genomicvariants')From CRAN and Bioconductor
install.packages('BiocManager')
BiocManager::install('methods')
BiocManager::install('ggplot2')
BiocManager::install('rmarkdown')
BiocManager::install('dplyr')
BiocManager::install('knitr')
BiocManager::install('RCurl')
BiocManager::install('VariantAnnotation')
BiocManager::install('BSgenome.Hsapiens.UCSC.hg19')
BiocManager::install('TxDb.Hsapiens.UCSC.hg19.knownGene')
BiocManager::install('SNPlocs.Hsapiens.dbSNP144.GRCh37')
BiocManager::install('GenomicFeatures')
BiocManager::install('maftools')
BiocManager::install('NMF')
BiocManager::install('BiocGenerics')
BiocManager::install('R.utils')
BiocManager::install('pheatmap')
BiocManager::install('stringr')
BiocManager::install('testthat')
BiocManager::install('yaml')The Presentations
Genomic Variant, Session 1
This section introduces the analysis of Genomic Variant in Bioconductor Session sections:
- Introduce VCF file structure
- Extract variant informations from VCF file
Links to presentations:
The html slide presentation can be found at this link Slide
The single page html presentation can be found at this link Single Page
The code use in the presentations can be found at R code
Genomic Variant, Session 2
This section demonstrates how to annotate variants by using TxDb and dbSNP Session sections:
- Annotate SNPs by using dbSNP
- Annotate variants in coding region
- Integrate information in a data frame
Links to presentations:
The html slide presentation can be found at this link Slide
The single page html presentation can be found at this link Single Page
The code use in the presentations can be found at R code
Genomic Variant, Session 3
This section demonstrates how to handle Variants from multiple samples and make advanced analysis Session sections:
- Introduce Mutation Annotatin Format (MAF)
- Load MAF file into R and make summary report
- Analysis of enrichment in genes, pathways, and mutational signatures
Links to presentations:
The html slide presentation can be found at this link Slide
The single page html presentation can be found at this link Single Page
The code use in the presentations can be found at R code
Getting help
Course help
For advice, help and comments for the material covered in this course please contact us at the issues page associated to this course.
The link to the help pages can be found here
General Bioinformatics support
If you would like contact us about general bioinformatics advice, support or collaboration, please contact us the Bioinformatics Resource Center at brc@rockefeller.edu.