In hms-dbmi/drugseqr.data: Data for 'dseqr' and 'rkal' Packages

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(dseqr.data)

Installation

dseqr.data can be installed from Bioconductor as follows:

if(!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("dseqr.data")

Overview of dseqr.data

dseqr.data includes: - experiment data from CMAP02 and L1000 for the dseqr package - annotation used by rkal for importing RNA-Seq data

Getting Started using dseqr.data

To load and download CMAP02 and L1000 data, dseqr does the following:

# to load the actual data replace 
# 'example.rds' with e.g. 'l1000_genes_es.rds'
drug_es <- load_drug_es('example.rds')

To generate transcript-to-gene maps for importing the results of kallisto quantification, rkal calls the following:

tx2gene <- load_tx2gene('Homo sapiens', release='94')

Session info

The following package and versions were used in the production of this vignette.

sessionInfo()

hms-dbmi/drugseqr.data documentation built on Oct. 23, 2024, 10:28 p.m.