DESCRIPTION

Package: rnaseqGene 
Title: RNA-seq workflow: gene-level exploratory analysis and differential expression
Version: 1.27.2
Date: 2020-01-04
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
LazyData: true
VignetteBuilder: knitr
biocViews: Workflow, GeneExpressionWorkflow, ImmunoOncologyWorkflow
Suggests: knitr, rmarkdown
NeedsCompilation: no
URL: https://github.com/thelovelab/rnaseqGene/