Package: customProDB
Type: Package
Title: Generate customized protein database from NGS data, with a focus
        on RNA-Seq data, for proteomics search
Version: 1.18.0
Date: 2017-04-16
Author: xiaojing wang
Maintainer: xiaojing wang <xiaojing.wang@bcm.edu>
Description: Database search is the most widely used approach for 
		peptide and protein identification in mass spectrometry-based 
		proteomics studies. Our previous study showed that 
		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 
		database more complete and sample-specific. Here, we report 
		an R package customProDB that enables the easy generation of 
		customized databases from RNA-Seq data for proteomics search. 
		This work bridges genomics and proteomics studies and 
		facilitates cross-omics data integration.
License: Artistic-2.0
Depends: R (>= 3.0.1), IRanges, AnnotationDbi, biomaRt
Imports: S4Vectors (>= 0.9.25), IRanges, GenomeInfoDb, GenomicRanges,
        Rsamtools (>= 1.10.2), GenomicAlignments, Biostrings (>=
        2.26.3), GenomicFeatures (>= 1.17.13), biomaRt (>= 2.17.1),
        stringr, RCurl, plyr, VariantAnnotation (>= 1.13.44),
        rtracklayer, RSQLite, AnnotationDbi, AhoCorasickTrie, methods
Suggests: BSgenome.Hsapiens.UCSC.hg19
LazyLoad: yes
biocViews: MassSpectrometry, Proteomics, SNP, RNASeq, Software,
        Transcription, AlternativeSplicing
NeedsCompilation: no
Packaged: 2017-10-31 00:44:40 UTC; biocbuild
Built: R 3.4.2; ; 2017-10-31 04:01:05 UTC; windows
