Package: rnaseqGene
Title: RNA-seq workflow: gene-level exploratory analysis and
        differential expression
Version: 1.37.0
Date: 2026-04-13
Authors@R: c(person(role=c("aut", "cre"), "Michael", "Love", email = "michaelisaiahlove@gmail.com"))
Description: Here we walk through an end-to-end gene-level RNA-seq
        differential expression workflow using Bioconductor packages.
        We will start from the FASTQ files, show how these were aligned
        to the reference genome, and prepare a count matrix which
        tallies the number of RNA-seq reads/fragments within each gene
        for each sample.  We will perform exploratory data analysis
        (EDA) for quality assessment and to explore the relationship
        between samples, perform differential gene expression analysis,
        and visually explore the results.
Depends: R (>= 3.3.0), BiocStyle, airway (>= 1.5.3), tximeta, magrittr,
        DESeq2, apeglm, vsn, dplyr, ggplot2, hexbin, pheatmap,
        RColorBrewer, PoiClaClu, glmpca, ggbeeswarm, genefilter,
        AnnotationDbi, org.Hs.eg.db, Gviz, sva, RUVSeq, fission
License: Artistic-2.0
Encoding: UTF-8
VignetteBuilder: knitr
biocViews: Workflow, GeneExpressionWorkflow, ImmunoOncologyWorkflow
Suggests: knitr, rmarkdown
NeedsCompilation: no
URL: https://github.com/thelovelab/rnaseqGene/
Config/pak/sysreqs: cmake make libbz2-dev libicu-dev libjpeg-dev
        liblzma-dev libpng-dev libuv1-dev libxml2-dev libssl-dev
        xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:43:10 UTC
RemoteUrl: https://github.com/bioc/rnaseqGene
RemoteRef: HEAD
RemoteSha: adf76f21025db6b414766adcdd1990f19e4d770f
Packaged: 2026-10-01 15:40:13 UTC; root
Author: Michael Love [aut, cre]
Maintainer: Michael Love <michaelisaiahlove@gmail.com>