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 online here

Course

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

{r} usethis::use_course("sa-lee/fluentGenomics")