customProDB
This is the released version of customProDB; for the devel version, see customProDB.
All Bioconductor versions of customProDB
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13
Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics search
Bioconductor version: 3.23 · Package version: 1.51.0
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"):
Xiaojing Wang. customProDB: Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics search. doi:10.18129/B9.bioc.customProDB, R package version 1.51.0, https://bioconductor.org/packages/customProDB.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") 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.
Details
| Version | 1.51.0 |
| License | Artistic-2.0 |
| In Bioconductor since | BioC 2.13 (R-3.0) (12 years) |
| Downloads rank | 1159 of 2,418 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | AlternativeSplicing, FunctionalGenomics, ImmunoOncology, MassSpectrometry, Proteomics, RNASeq, SNP, Sequencing, Software, Transcription |
| Package Short Url | https://bioconductor.org/packages/customProDB/ |
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 |
Download
Follow the installation instructions to use this package in your R session.
| Source package | customProDB_1.51.0.tar.gz |
| Windows binary (x86_64) | customProDB_1.51.0.zip |
| macOS binary (arm64) | customProDB_1.51.0.tgz |
| macOS binary (x86_64) | customProDB_1.51.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/customProDB |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/customProDB |
| Package Downloads Report | Download Stats |
Dependencies
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
Suggests: RMariaDB, BSgenome.Hsapiens.UCSC.hg19