Package: RCAS
Type: Package
Title: RNA Centric Annotation System
Version: 1.5.4
Date: 2018-02-27
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 automated system that provides dynamic genome 
    annotations for custom input files that contain transcriptomic regions. 
    Such transcriptomic regions could be, for instance, peak regions 
    detected by CLIP-Seq analysis that detect protein-RNA interactions, 
    RNA modifications (alias the epitranscriptome), CAGE-tag locations, or 
    any other collection of target regions at the level of the 
    transcriptome. RCAS is designed as a reporting tool for the functional 
    analysis of RNA-binding sites detected by high-throughput experiments. 
    It takes as input a BED format file containing the genomic coordinates 
    of the RNA binding sites and a GTF file that contains the genomic 
    annotation features usually provided by publicly available databases 
    such as Ensembl and UCSC. RCAS performs overlap operations between 
    the genomic coordinates of the RNA binding sites and the genomic 
    annotation features and produces in-depth annotation summaries 
    such as the distribution of binding sites with respect to gene features 
    (exons, introns, 5'/3' UTR regions, exon-intron boundaries, promoter 
    regions, and whole transcripts). Moreover, by detecting the collection of 
    targeted transcripts, RCAS can carry out functional annotation tables for 
    enriched gene sets (annotated by the Molecular Signatures Database) and 
    GO terms. As one of the most important questions that arise during 
    protein-RNA interaction analysis; RCAS has a module for detecting 
    sequence motifs enriched in the targeted regions of the transcriptome.
    A full interactive report in HTML format can be generated that contains 
    interactive figures and tables that are ready for publication purposes.
License: Artistic-2.0
LazyData: TRUE
Depends: R (>= 3.3.0), plotly (>= 4.5.2), DT (>= 0.2), data.table,
        topGO, motifRG
Imports: biomaRt, AnnotationDbi, GenomicRanges,
        BSgenome.Hsapiens.UCSC.hg19, GenomeInfoDb (>= 1.12.0),
        Biostrings, rtracklayer, org.Hs.eg.db, GenomicFeatures,
        rmarkdown (>= 0.9.5), genomation (>= 1.5.5), knitr (>= 1.12.3),
        BiocGenerics, S4Vectors, stats, plotrix, pbapply, RSQLite,
        proxy, DBI, pheatmap, ggplot2, cowplot, ggseqlogo, methods,
        utils
RoxygenNote: 6.0.1
Suggests: BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10,
        BSgenome.Mmusculus.UCSC.mm9, BSgenome.Celegans.UCSC.ce10,
        BSgenome.Dmelanogaster.UCSC.dm3, org.Mm.eg.db, org.Ce.eg.db,
        org.Dm.eg.db, testthat, covr
SystemRequirements: pandoc (>= 1.12.3)
VignetteBuilder: knitr
biocViews: Software, GeneTarget, MotifAnnotation, MotifDiscovery, GO,
        Transcriptomics, GenomeAnnotation, GeneSetEnrichment, Coverage
Author: Bora Uyar [aut, cre],
  Dilmurat Yusuf [aut],
  Ricardo Wurmus [aut],
  Altuna Akalin [aut]
Maintainer: Bora Uyar <bora.uyar@mdc-berlin.de>
Built: R 3.4.1; ; 2018-03-27 17:45:51 UTC; unix
