GitHub - sa-lee/fluentGenomics: plyranges and tximeta case study (original) (raw)

Fluent genomics with plyranges and tximeta

In fluentGenomics we explore the use of the Bioconductor packages plyranges and tximeta through integrating results from an experiment using RNA-seq and ATAC-seq data. Readers will learn how to perform genomic range based operations in a principled way using plyranges and how to cleanly import quantification and differential expression data into R using tximeta.

Installation

The fluentGenomics package is available on Bioconductor:

install.packages("BiocManager")

BiocManager::install('fluentGenomics')

To install fluentGenomics from github with associated dependencies use

BiocManager::install('sa-lee/fluentGenomics', build_vignettes = TRUE, dependencies = TRUE)

To install fluentGenomics from Bioconductor's devel branch use:

BiocManager::install('fluentGenomics', version = 'devel')

Workflow

Once the package has been installed, you can work through the vignette directly from R/Rstudio with:

vignette("fluentGenomics")

Or you can read it onlinehere

Course

You can use the package as course material directly with the usethispackage:

usethis::use_course("sa-lee/fluentGenomics")