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customProDB

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


Bioconductor version: Release (3.18)

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 <xwang.research at gmail.com> Bo Wen <wenbostar at gmail.com>

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

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("customProDB")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

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

browseVignettes("customProDB")
Introduction to customProDB PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews AlternativeSplicing, FunctionalGenomics, ImmunoOncology, MassSpectrometry, Proteomics, RNASeq, SNP, Sequencing, Software, Transcription
Version 1.41.0
In Bioconductor since BioC 2.13 (R-3.0) (10.5 years)
License Artistic-2.0
Depends R (>= 3.5.0), IRanges, AnnotationDbi, biomaRt(>= 2.17.1)
Imports S4Vectors(>= 0.9.25), DBI, GenomeInfoDb, GenomicRanges, Rsamtools(>= 1.10.2), GenomicAlignments, Biostrings(>= 2.26.3), GenomicFeatures(>= 1.32.0), stringr, RCurl, plyr, VariantAnnotation(>= 1.13.44), rtracklayer, RSQLite, AhoCorasickTrie, methods
System Requirements
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Suggests RMariaDB, BSgenome.Hsapiens.UCSC.hg19
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Package Archives

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

Source Package customProDB_1.41.0.tar.gz
Windows Binary customProDB_1.41.0.zip
macOS Binary (x86_64) customProDB_1.41.0.tgz
macOS Binary (arm64) customProDB_1.41.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/customProDB
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/customProDB
Bioc Package Browser https://code.bioconductor.org/browse/customProDB/
Package Short Url https://bioconductor.org/packages/customProDB/
Package Downloads Report Download Stats