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 (3.21)

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 "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	AlternativeSplicing, FunctionalGenomics, ImmunoOncology, MassSpectrometry, Proteomics, RNASeq, SNP, Sequencing, Software, Transcription
Version	1.47.0
In Bioconductor since	BioC 2.13 (R-3.0) (11 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, txdbmaker, AhoCorasickTrie, methods
System Requirements
URL

Suggests	RMariaDB, BSgenome.Hsapiens.UCSC.hg19
Linking To
Enhances
Depends On Me
Imports Me
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Build Report	Build Report

Package Archives

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

Source Package	customProDB_1.47.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
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