Package: RCAS
Type: Package
Title: RNA Centric Annotation System
Version: 1.36.0
Date: 2024-03-19
Authors@R: c(person("Bora", "Uyar", email='bora.uyar@mdc-berlin.de', role=c("aut", "cre")),
              person("Dilmurat", "Yusuf", role=c("aut")),
              person("Ricardo", "Wurmus", role=c("aut")),
              person("Altuna", "Akalin", role=c("aut")))
Description: RCAS is an R/Bioconductor package designed as a generic
        reporting tool for the functional analysis of
        transcriptome-wide regions of interest detected by
        high-throughput experiments. Such transcriptomic regions could
        be, for instance, signal peaks detected by CLIP-Seq analysis
        for protein-RNA interaction sites, RNA modification sites
        (alias the epitranscriptome), CAGE-tag locations, or any other
        collection of query regions at the level of the transcriptome.
        RCAS produces in-depth annotation summaries and coverage
        profiles based on the distribution of the query regions with
        respect to transcript features (exons, introns, 5'/3' UTR
        regions, exon-intron boundaries, promoter regions). Moreover,
        RCAS can carry out functional enrichment analyses and
        discriminative motif discovery.
License: Artistic-2.0
LazyData: TRUE
Depends: R (>= 3.5.0), plotly (>= 4.5.2), DT (>= 0.2), data.table
Imports: GenomicRanges, IRanges, BSgenome, BSgenome.Hsapiens.UCSC.hg19,
        GenomeInfoDb (>= 1.12.0), Biostrings, rtracklayer,
        GenomicFeatures, txdbmaker, rmarkdown (>= 0.9.5), genomation
        (>= 1.5.5), knitr (>= 1.12.3), BiocGenerics, S4Vectors,
        plotrix, pbapply, RSQLite, proxy, pheatmap, ggplot2, cowplot,
        seqLogo, utils, ranger, gprofiler2
RoxygenNote: 7.3.1
Suggests: testthat, covr, BiocManager
SystemRequirements: pandoc (>= 1.12.3)
VignetteBuilder: knitr
biocViews: Software, GeneTarget, MotifAnnotation, MotifDiscovery, GO,
        Transcriptomics, GenomeAnnotation, GeneSetEnrichment, Coverage
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libpng-dev
        libxml2-dev libssl-dev libx11-dev xz-utils zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:33:22 UTC
RemoteUrl: https://github.com/bioc/RCAS
RemoteRef: RELEASE_3_22
RemoteSha: 780ed18456feccd9bb7ad954068de3b7b5904cc4
NeedsCompilation: no
Packaged: 2026-01-24 21:34:52 UTC; root
Author: Bora Uyar [aut, cre],
  Dilmurat Yusuf [aut],
  Ricardo Wurmus [aut],
  Altuna Akalin [aut]
Maintainer: Bora Uyar <bora.uyar@mdc-berlin.de>
Built: R 4.5.2; ; 2026-01-24 21:38:11 UTC; windows
