DESCRIPTION

Package: RCAS
Type: Package
Title: RNA Centric Annotation System
Version: 1.29.3
Date: 2021-11-21
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 (>= 3.3.0),
    plotly (>= 4.5.2),
    DT (>= 0.2),
    data.table,
Imports:
    GenomicRanges,
    IRanges,
    BSgenome, 
    BSgenome.Hsapiens.UCSC.hg19,
    GenomeInfoDb (>= 1.12.0),
    Biostrings,
    rtracklayer,
    GenomicFeatures,
    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: 7.2.3
Suggests: testthat,
    covr,
    BiocManager
SystemRequirements: pandoc (>= 1.12.3)
VignetteBuilder: knitr
biocViews: Software, GeneTarget, MotifAnnotation, MotifDiscovery, GO, Transcriptomics, GenomeAnnotation, GeneSetEnrichment, Coverage