Package: diffwrap
Type: Package
Title: Differential Expression Analysis of RNA-Seq Data
Version: 0.6-3
Date: 2026-08-10
Authors@R: person(list("Vidal", "Meeri", "Reija", "Bogdan", "Adrien"), list("Fey", "Pekkarinen", "Hieta", "Iancu", "Janssens"), email = list("vidal.fey@gmail.com", "meeri.pekkarinen@gmail.com", "reija.hieta@geneviatechnologies.com", "bogdan.iancu@abo.fi", "Adrien.RFM.Janssens@proton.me"), role = list(c("aut", "cre"), "aut", "aut", "aut", "aut"))
Description: Functions for differential expression analysis of read
        counts from messenger RNA (mRNA) sequencing (RNA-Seq) data or
        micro RNA (miRNA) expression values generated by the
        Comprehensive Analysis Pipeline for microRNA Sequencing
        (CAP-miRSeq) 'expression_reports.sh' script. The workflow
        follows the 'edgeR'-'limma' expression data analysis pipeline
        providing options for different approaches, such as "pure"
        'edgeR', voom or paired samples. The functions in the package
        generate text files with differential expression lists,
        optionally annotated with information from 'biomart',
        expression summary plots as well as several quality control
        (QC) plots. The main function, diffExpr(), is a convenience
        wrapper performing all steps automatically based on sensible
        defaults. Methods are described in Robinson, McCarthy and Smyth
        (2010) <doi:10.1093/bioinformatics/btp616>, Ritchie et al.
        (2015) <doi:10.1093/nar/gkv007>, Law et al. (2014)
        <doi:10.1186/gb-2014-15-2-r29> and Sun et al. (2014)
        <doi:10.1186/1471-2164-15-423>.
Maintainer: Vidal Fey <vidal.fey@gmail.com>
Depends: R (>= 4.0.0)
Imports: plyr, ggplot2, edgeR, limma, RColorBrewer, convertid (>=
        0.3.4), pheatmap, ggrepel, data.table, magrittr, methods,
        Hmisc, ltm, openxlsx, purrr, dplyr, venn, VennDiagram, grid,
        scales
Suggests: testthat (>= 3.0.0), withr, futile.logger, rappdirs, knitr,
        quarto, dendextend, rmarkdown, AnnotationDbi, org.Hs.eg.db,
        org.Mm.eg.db, clusterProfiler, gprofiler2, topGO, igraph,
        scatterplot3d, readxl, WriteXLS, biomaRt
License: GPL-3
Encoding: UTF-8
LazyData: true
VignetteBuilder: quarto
NeedsCompilation: no
Author: Vidal Fey [aut, cre], Meeri Pekkarinen [aut], Reija Hieta
        [aut], Bogdan Iancu [aut], Adrien Janssens [aut]
Config/roxygen2/version: 8.0.0
Packaged: 2026-09-29 12:51:01 UTC; root
Config/pak/sysreqs: zlib1g-dev
Repository: https://cran.r-universe.dev
Date/Publication: 2026-08-30 13:00:50 UTC
RemoteUrl: https://github.com/cran/diffwrap
RemoteRef: HEAD
RemoteSha: 27e8b17c4356ad19204cc427f71dbc2dd7b8033e