A plyranges and tximeta workflow (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')
Once the package has been installed, you can work through the vignette directly from R/Rstudio with:
Or you can read it online here
Links
- Download from BIOC at
https://www.bioconductor.org/packages/fluentGenomics - Browse source code at
https://github.com/sa-lee/fluentGenomics/ - Report a bug at
https://github.com/sa-lee/fluentGenomics/issues
