customProDB
Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics search
Bioconductor version: Release (3.19)
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("customProDB")):
Installation
To install this package, start R (version "4.4") 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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | AlternativeSplicing, FunctionalGenomics, ImmunoOncology, MassSpectrometry, Proteomics, RNASeq, SNP, Sequencing, Software, Transcription |
| Version | 1.44.0 |
| 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 |
See More
| Suggests | RMariaDB, BSgenome.Hsapiens.UCSC.hg19 |
| Linking To | |
| Enhances | |
| 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_1.44.0.tar.gz |
| Windows Binary (x86_64) | customProDB_1.44.0.zip |
| macOS Binary (x86_64) | customProDB_1.44.0.tgz |
| macOS Binary (arm64) | customProDB_1.44.0.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 |