Package: customProDB Type: Package Title: Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics search Version: 1.53.0 Date: 2024-04-03 Author: Xiaojing Wang Maintainer: Xiaojing Wang Bo Wen 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: 2026-04-28 12:37:48 UTC RemoteUrl: https://github.com/bioc/customProDB RemoteRef: HEAD RemoteSha: 578e4c597de34aa45ad2433c19e93f6f2b0c71c8 NeedsCompilation: no Packaged: 2026-06-15 07:09:45 UTC; root