customProDB

Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics search.

Bioconductor version: Release (2.14)

Generate customized protein sequence database from RNA-Seq data for proteomics search

Author: xiaojing wang

Maintainer: xiaojing wang <xiaojing.wang at vanderbilt.edu>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("customProDB")

To cite this package in a publication, start R and enter:

    citation("customProDB")

Documentation

PDF R Script Introduction to customProDB
PDF   Reference Manual

Details

biocViews Proteomics, Software
Version 1.4.0
In Bioconductor since BioC 2.13 (R-3.0)
License Artistic-2.0
Depends R (>= 3.0.1), IRanges, AnnotationDbi, biomaRt
Imports IRanges, GenomicRanges, Rsamtools(>= 1.10.2), GenomicAlignments, Biostrings(>= 2.26.3), GenomicFeatures(>= 1.13.15), biomaRt(>= 2.17.1), stringr, RCurl, plyr, VariantAnnotation(>= 1.7.28), rtracklayer, RSQLite, AnnotationDbi
Suggests BSgenome.Hsapiens.UCSC.hg19
System Requirements
URL
Depends On Me
Imports Me
Suggests Me

Package Downloads

Package Source customProDB_1.4.0.tar.gz
Windows Binary customProDB_1.4.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) customProDB_1.4.0.tgz
Mac OS X 10.9 (Mavericks)
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