Package: bambamR
Title: End-to-End RNA-Seq Processing from FASTQ to Publication-Ready
        Plots
Version: 0.1.0
Authors@R: c(
    person("R.", "Heller",
           email = "raban.heller@uni-ulm.de",
           role = c("aut", "cre"),
           comment = c(ORCID = "0000-0001-8006-9742")),
    person("Hanno", "Witte", role = "aut"),
    person("Konrad", "Steinestel", role = "aut")
    )
Description: A streamlined toolkit for RNA-seq analysis covering
        FASTQ/BAM import, quality control, alignment, read counting,
        normalization, differential expression analysis, and
        publication-ready visualizations including onco plots, volcano
        plots, heatmaps, and PCA. Operates in minimal mode with
        CRAN-only dependencies or in full mode when Bioconductor
        packages are available.
Depends: R (>= 4.1.0)
Imports: ggplot2 (>= 3.4.0), data.table, stats, utils, grDevices,
        methods
Suggests: BiocManager, ShortRead, Biostrings, Rsamtools,
        GenomicAlignments, GenomicFeatures, txdbmaker, GenomicRanges,
        DESeq2, edgeR, limma, SummarizedExperiment, Biobase,
        ComplexHeatmap, pheatmap, patchwork, ggrepel, shiny,
        shinydashboard, bslib, DT, testthat (>= 3.0.0), knitr,
        rmarkdown, withr
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
VignetteBuilder: knitr
URL: https://cttir.github.io/bambamR/, https://github.com/cttir/bambamR
BugReports: https://github.com/cttir/bambamR/issues
Config/testthat/edition: 3
Config/Needs/website: CTTIR/themakR, pkgdown
Config/roxygen2/version: 8.0.0
Repository: https://cttir.r-universe.dev
Date/Publication: 2026-11-03 11:57:15 UTC
RemoteUrl: https://github.com/CTTIR/bambamR
RemoteRef: HEAD
RemoteSha: 4e286818259d2dd08858b912b430172cee62d5e0
NeedsCompilation: no
Packaged: 2026-11-03 18:06:27 UTC; root
Author: R. Heller [aut, cre] (ORCID: <https://orcid.org/0000-0001-8006-9742>),
  Hanno Witte [aut],
  Konrad Steinestel [aut]
Maintainer: R. Heller <raban.heller@uni-ulm.de>