To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("customProDB")

In most cases, you don't need to download the package archive at all.

customProDB

 

   

This is the development version of customProDB; for the stable release version, see customProDB.

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

Bioconductor version: Development (3.6)

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.

Author: xiaojing wang

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

Citation (from within R, enter citation("customProDB")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("customProDB")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("customProDB")

 

PDF R Script Introduction to customProDB
PDF   Reference Manual
Text   NEWS

Details

biocViews AlternativeSplicing, MassSpectrometry, Proteomics, RNASeq, SNP, Software, Transcription
Version 1.17.0
In Bioconductor since BioC 2.13 (R-3.0) (3.5 years)
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
LinkingTo
Suggests BSgenome.Hsapiens.UCSC.hg19
SystemRequirements
Enhances
URL
Depends On Me
Imports Me PGA
Suggests Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source customProDB_1.17.0.tar.gz
Windows Binary customProDB_1.17.0.zip
Mac OS X 10.11 (El Capitan) customProDB_1.17.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/customProDB
Package Short Url http://bioconductor.org/packages/customProDB/
Package Downloads Report Download Stats

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