Package: customProDB
Type: Package
Title: Generate customized protein database from NGS data, with a focus
        on RNA-Seq data, for proteomics search
Version: 1.51.0
Date: 2024-04-03
Author: Xiaojing Wang
Maintainer: Xiaojing Wang <xwang.research@gmail.com> Bo Wen
 <wenbostar@gmail.com>
Description: 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.
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
Suggests: RMariaDB, BSgenome.Hsapiens.UCSC.hg19
LazyLoad: yes
biocViews: ImmunoOncology, Sequencing, MassSpectrometry, Proteomics,
        SNP, RNASeq, Software, Transcription, AlternativeSplicing,
        FunctionalGenomics
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libpng-dev
        libxml2-dev libssl-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 14:15:09 UTC
RemoteUrl: https://github.com/bioc/customProDB
RemoteRef: HEAD
RemoteSha: 8317345edba19683936f5f036d26e5fee7988672
NeedsCompilation: no
Packaged: 2026-03-10 08:50:21 UTC; root
Built: R 4.6.0; ; 2026-03-10 08:53:15 UTC; windows
