Package: rsemflow
Type: Package
Title: Metadata-Driven Downstream Analysis for RSEM Gene-Level Results
Version: 0.1.1
Authors@R: person("Daiki", "Kumakura", role = c("aut", "cre"),
    email = "55353329+DaikiKumakura@users.noreply.github.com")
Description: A command-line and R interface for reproducible downstream
        analysis of RSEM gene-level expression estimates. 'rsemflow'
        imports '*.genes.results' files together with ordinary sample
        metadata, computes expression-level summaries, normalization,
        principal component analysis, sample correlation, 'DESeq2'
        differential expression, preranked gene set enrichment
        analysis, 'GSVA' or 'ssGSEA' pathway scores, and Ensembl gene
        annotation. Every result is written as a tab-separated table;
        the package does not draw figures.
License: MIT + file LICENSE
URL: https://daikikumakura.github.io/rsemflow/,
        https://github.com/DaikiKumakura/rsemflow
BugReports: https://github.com/DaikiKumakura/rsemflow/issues
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
biocViews: RNASeq, DifferentialExpression, GeneSetEnrichment,
        Transcriptomics
Depends: R (>= 4.3.0)
Imports: AnnotationDbi, BiocParallel, DESeq2, GSVA (>= 2.0.0),
        SummarizedExperiment, data.table, fgsea, msigdbr (>= 10.0.0),
        stats, tools, tximport, utils
Suggests: knitr, org.Hs.eg.db, org.Mm.eg.db, rmarkdown, testthat (>=
        3.0.0)
VignetteBuilder: knitr
Config/testthat/edition: 3
Config/pak/sysreqs: libmagick++-dev gsfonts libicu-dev libpng-dev
        libxml2-dev libssl-dev zlib1g-dev
Repository: https://daikikumakura.r-universe.dev
Date/Publication: 2026-10-18 23:48:59 UTC
RemoteUrl: https://github.com/DaikiKumakura/rsemflow
RemoteRef: HEAD
RemoteSha: 66f38bb6c804293d672d63fd4d94f3b03fdf6112
NeedsCompilation: no
Packaged: 2026-10-22 11:59:26 UTC; root
Author: Daiki Kumakura [aut, cre]
Maintainer: Daiki Kumakura <55353329+DaikiKumakura@users.noreply.github.com>