DESCRIPTION

Package: customProDB
Type: Package
Title: Generate customized protein databases from NGS data for proteomics search
Version: 1.16.2
Date: 2017-02-08
Authors@R: c(person("Xiaojing", "Wang", email="xiaojing.wang@bcm.edu", role=c("aut", "cre")),
    person("Matt", "Chambers", email="matt.chambers42@gmail.com", role=c("aut", "cph")),
    person("Baylor College of Medicine", role="cph"),
    person("Vanderbilt University", role="cph"))
Description: Database search is the most widely used approach for peptide and protein identification in mass-
    spectrometry-based proteomics studies. Sample-specific protein databases derived from RNA-Seq data can 
    better approximate the real protein pools in the samples and thus improve protein identification. 
    More importantly, single nucleotide variations, short insertion and deletions and novel junctions 
    identified from RNA-Seq data make protein databases more complete and sample-specific. CustomProDB 
    enables the easy generation of customized databases from RNA-Seq data for proteomics search. It bridges 
    genomics and proteomics studies and facilitates cross-omics data integration.
License: Artistic-2.0
Depends:
    R (>= 3.0.1)
Imports:
    methods,
    Biobase,
    S4Vectors (>= 0.9.25),
    IRanges,
    GenomeInfoDb,
    GenomicRanges,
    Rsamtools (>= 1.10.2),
    GenomicAlignments,
    Biostrings (>= 2.26.3),
    GenomicFeatures (>= 1.26.4),
    SummarizedExperiment,
    biomaRt (>= 2.17.1),
    stringr,
    stringi,
    RCurl,
    plyr,
    VariantAnnotation (>= 1.20.3),
    rtracklayer,
    RSQLite,
    AnnotationDbi,
    data.table,
    DBI,
    RMySQL,
    sqldf,
    testthat,
    GetoptLong
Suggests:
    BSgenome.Hsapiens.UCSC.hg19,
    covr,
    diffobj
LazyLoad: yes
biocViews: MassSpectrometry, Proteomics, SNP, RNASeq, Software, Transcription,
    AlternativeSplicing
RoxygenNote: 6.0.1