hms-dbmi/drugseqr: GUI to Explore Single-Cell and Bulk RNA-Seq from Fastq to Pathways and Perturbations

GUI to import and explore single-cell and bulk RNA-seq datasets and run queries to find similar and opposing L1000 and CMAP02 perturbation signatures. Single-cell fastq files can be quantified, imported, QC'ed, annotated and integrated. For integrated datasets, 'limma' pseudobulk differential expression results can be explored within the app or downloaded along with pathway and differential abundance analyses. Bulk RNA-seq fastq files can also be quantified, imported, analysed, and deconvoluted using a single-cell dataset. Finally, differential expression analyses from bulk and single-cell datasets can be used to find similar and opposing CMAP02 and L1000 perturbation signatures.

Getting started

Package details

AuthorAlex Pickering
MaintainerAlex Pickering <alexvpickering@gmail.com>
LicenseMIT + file LICENSE
Version0.15.8
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
install.packages("remotes")
remotes::install_github("hms-dbmi/drugseqr")
hms-dbmi/drugseqr documentation built on Aug. 2, 2021, 9:56 a.m.