Registration Open for Bioc2024 July 24-26


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 (3.20)

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> Bo Wen <wenbostar at>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


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


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

Introduction to customProDB PDF R Script
Reference Manual PDF


biocViews AlternativeSplicing, FunctionalGenomics, ImmunoOncology, MassSpectrometry, Proteomics, RNASeq, SNP, Sequencing, Software, Transcription
Version 1.45.0
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, txdbmaker, AhoCorasickTrie, methods
System Requirements
See More
Suggests RMariaDB, BSgenome.Hsapiens.UCSC.hg19
Linking To
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package customProDB_1.45.0.tar.gz
Windows Binary
macOS Binary (x86_64) customProDB_1.45.0.tgz
macOS Binary (arm64) customProDB_1.45.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats