Prework

R/Bioconductor for Bioinformatics

Before attending the workshop please have the following installed and configured on your machine.

• Recent version of R

• Recent version of RStudio

• Most recent release of the Bioconductor and other packages used in courses

Install the latest release of R, then get the latest version of Bioconductor by starting R and entering the commands.

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(version = "3.16")

• Ensure you can knit R markdown documents

  • Open RStudio and create a new Rmarkdown document
  • Save the document and check you are able to knit it.

Install Bioconductor Packages

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install()

Install specific packages, e.g., “GenomicFeatures” and “AnnotationDbi”, with

BiocManager::install(c("GenomicFeatures", "AnnotationDbi"))

The install() function (in the BiocManager package) has arguments that change its default behavior; type ?install for further help.

Posit cloud is free of charge for personal users, yet you need to sign up for a new user account and have internet connection.

Packages

install.packages('BiocManager')
BiocManager::install('methods')
BiocManager::install('rmarkdown')
BiocManager::install('igraph')
BiocManager::install('org.Hs.eg.db')
BiocManager::install('RMariaDB')
BiocManager::install('Rbowtie')
BiocManager::install('parallel')
BiocManager::install('QuasR')
BiocManager::install('BSgenome')
BiocManager::install('BSgenome.Mmusculus.UCSC.mm10')
BiocManager::install('BSgenome.Hsapiens.UCSC.hg19')
BiocManager::install('BSgenome.Hsapiens.UCSC.hg38')
BiocManager::install('Biostrings')
BiocManager::install('rtracklayer')
BiocManager::install('ggplot2')
BiocManager::install('GenomicRanges')
BiocManager::install('ShortRead')
BiocManager::install('Rsubread')
BiocManager::install('Rsamtools')
BiocManager::install('Rbowtie2')
BiocManager::install('stringi')
BiocManager::install('Rhisat2')
BiocManager::install('R.utils')
BiocManager::install('GenomicAlignments')
BiocManager::install('basecallQC')
BiocManager::install('TxDb.Mmusculus.UCSC.mm10.knownGene')
BiocManager::install('TxDb.Hsapiens.UCSC.hg19.knownGene')
BiocManager::install('Rfastp')
BiocManager::install('TxDb.Hsapiens.UCSC.hg38.knownGene')
BiocManager::install('knitr')
BiocManager::install('testthat')
BiocManager::install('yaml')

Data

The datasets we use can be found here https://github.com/omicscenter/RforBioinformatics.

Code

The R scripts used in part 1 and part 2 can be found here https://github.com/omicscenter/RforBioinformatics.

Resources

Lecture notes https://github.com/omicscenter/RforBioinformatics

Lab notes https://github.com/omicscenter/RforBioinformatics