{ "_id": "6a1e94a01d7bb097a0a6b3dc", "Package": "customProDB", "Type": "Package", "Title": "Generate customized protein database from NGS data, with a focus\non RNA-Seq data, for proteomics search", "Version": "1.52.0", "Date": "2024-04-03", "Author": "Xiaojing Wang", "Maintainer": "Xiaojing Wang Bo Wen\n", "Description": "Database search is the most widely used approach for\npeptide and protein identification in mass spectrometry-based\nproteomics studies. Our previous study showed that\nsample-specific protein databases derived from RNA-Seq data can\nbetter approximate the real protein pools in the samples and\nthus improve protein identification. More importantly, single\nnucleotide variations, short insertion and deletions and novel\njunctions identified from RNA-Seq data make protein database\nmore complete and sample-specific. Here, we report an R package\ncustomProDB that enables the easy generation of customized\ndatabases from RNA-Seq data for proteomics search. This work\nbridges genomics and proteomics studies and facilitates\ncross-omics data integration.", "License": "Artistic-2.0", "LazyLoad": "yes", "biocViews": "ImmunoOncology, Sequencing, MassSpectrometry, Proteomics,\nSNP, RNASeq, Software, Transcription, AlternativeSplicing,\nFunctionalGenomics", "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libpng-dev\nlibxml2-dev libssl-dev xz-utils zlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:37:48 UTC", "RemoteUrl": "https://github.com/bioc/customProDB", "RemoteRef": "RELEASE_3_23", "RemoteSha": "2024add18a7957678e3866a09d9acbc31456d418", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-02 08:17:49 UTC", "User": "root" }, "MD5sum": "c3489372b8db20e19a849e56c9885e76", "_user": "bioc-release", "_type": "src", "_file": "customProDB_1.52.0.tar.gz", "_fileid": "611032f115804d2ce99e5be09ed9f5cdacdf16a3407b080d1a521ec51cd7591c", "_filesize": 696852, "_sha256": "611032f115804d2ce99e5be09ed9f5cdacdf16a3407b080d1a521ec51cd7591c", "_created": "2026-06-02T08:17:49.000Z", "_published": "2026-06-02T08:30:24.592Z", "_jobs": [ { "job": 79028681912, "time": 268, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7352591630" }, { "job": 79028681959, "time": 594, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "7352700728" }, { "job": 79028682128, "time": 640, "config": "linux-release-x86_64", "r": "4.6.0", "check": "ERROR", "artifact": "7352715995" }, { "job": 79028681957, "time": 573, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "ERROR", "artifact": "7352693709" }, { "job": 79028681995, "time": 638, "config": "macos-release-arm64", "r": "4.6.0", "check": "ERROR", "artifact": "7352715001" }, { "job": 79027644447, "time": 385, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7352500131" }, { "job": 79028681970, "time": 188, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7352565264" }, { "job": 79028681924, "time": 541, "config": "windows-devel", "r": "4.7.0", "check": "ERROR", "artifact": "7352683565" }, { "job": 79028681940, "time": 554, "config": "windows-oldrel", "r": "4.5.3", "check": "ERROR", "artifact": "7352687523" }, { "job": 79028682006, "time": 663, "config": "windows-release", "r": "4.6.0", "check": "ERROR", "artifact": "7352723743" } ], "_bioccheck": { "error": 2, "warning": 2, "note": 16 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26807186884", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/customProDB", "_commit": { "id": "2024add18a7957678e3866a09d9acbc31456d418", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777379868 }, "_maintainer": { "name": "Xiaojing Wang", "email": "wenbostar@gmail.com", "login": "wangx15", "description": "", "uuid": 38963445 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "IRanges", "role": "Depends" }, { "package": "AnnotationDbi", "role": "Depends" }, { "package": "biomaRt", "version": ">= 2.17.1", "role": "Depends" }, { "package": "S4Vectors", "version": ">= 0.9.25", "role": "Imports" }, { "package": "DBI", "role": "Imports" }, { "package": "GenomeInfoDb", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "Rsamtools", "version": ">= 1.10.2", "role": "Imports" }, { "package": "GenomicAlignments", "role": "Imports" }, { "package": "Biostrings", "version": ">= 2.26.3", "role": "Imports" }, { "package": "GenomicFeatures", "version": ">= 1.32.0", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "RCurl", "role": "Imports" }, { "package": "plyr", "role": "Imports" }, { "package": "VariantAnnotation", "version": ">= 1.13.44", "role": "Imports" }, { "package": "rtracklayer", "role": "Imports" }, { "package": "RSQLite", "role": "Imports" }, { "package": "txdbmaker", "role": "Imports" }, { "package": "AhoCorasickTrie", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "RMariaDB", "role": "Suggests" }, { "package": "BSgenome.Hsapiens.UCSC.hg19", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.53.0", "bioc": "3.24" }, { "branch": "release", "version": "1.51.0", "bioc": "3.23" } ], "_topics": [ "immunooncology", "sequencing", "massspectrometry", "proteomics", "snp", "rnaseq", "software", "transcription", "alternativesplicing", "functionalgenomics" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 380, "source": "https://www.bioconductor.org/packages/stats/bioc/customProDB" }, "_mentions": 7, "_searchresults": 18, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/customProDB.html", "extra/NEWS.html", "extra/NEWS.txt", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "aaVariation", "Bed2Range", "calculateRPKM", "easyRun", "easyRun_mul", "InputVcf", "JunctionType", "Multiple_VCF", "Outputaberrant", "OutputNovelJun", "Outputproseq", "OutputsharedPro", "OutputVarprocodingseq", "OutputVarproseq", "OutputVarproseq_single", "Positionincoding", "PrepareAnnotationEnsembl", "PrepareAnnotationRefseq", "SharedJunc", "Varlocation" ], "_help": [ { "page": "aaVariation", "title": "get the functional consequencece of SNVs located in coding region", "topics": [ "aaVariation" ] }, { "page": "Bed2Range", "title": "Generate a GRanges objects from BED file.", "topics": [ "Bed2Range" ] }, { "page": "calculateRPKM", "title": "Caculate RPKM for each transcripts based on exon read counts.", "topics": [ "calculateRPKM" ] }, { "page": "easyRun", "title": "An integrated function to generate customized protein database for a single sample", "topics": [ "easyRun" ] }, { "page": "easyRun_mul", "title": "An integrated function to generate consensus protein database from multiple samples", "topics": [ "easyRun_mul" ] }, { "page": "InputVcf", "title": "Generate a list of GRanges objects from a VCF file.", "topics": [ "InputVcf" ] }, { "page": "JunctionType", "title": "Annotates the junctions in a bed file.", "topics": [ "JunctionType" ] }, { "page": "Multiple_VCF", "title": "Generate shared variation dataset from multiple VCF files", "topics": [ "Multiple_VCF" ] }, { "page": "Outputaberrant", "title": "generate FASTA file containing short INDEL", "topics": [ "Outputaberrant" ] }, { "page": "OutputNovelJun", "title": "generate peptide FASTA file that contains novel junctions.", "topics": [ "OutputNovelJun" ] }, { "page": "Outputproseq", "title": "output FASTA format file contains proteins that have expression level above the cutoff", "topics": [ "Outputproseq" ] }, { "page": "OutputsharedPro", "title": "Output the sequences of proteins with high expressions in multiple samples.", "topics": [ "OutputsharedPro" ] }, { "page": "OutputVarprocodingseq", "title": "Output the variant(SNVs) protein coding sequences", "topics": [ "OutputVarprocodingseq" ] }, { "page": "OutputVarproseq", "title": "Output the variant(SNVs) protein sequences into FASTA format", "topics": [ "OutputVarproseq" ] }, { "page": "OutputVarproseq_single", "title": "Output the variant(SNVs) protein sequences into FASTA format", "topics": [ "OutputVarproseq_single" ] }, { "page": "Positionincoding", "title": "Find the position in coding sequence for each variation.", "topics": [ "Positionincoding" ] }, { "page": "PrepareAnnotationEnsembl", "title": "prepare annotation from ENSEMBL", "topics": [ "PrepareAnnotationEnsembl" ] }, { "page": "PrepareAnnotationRefseq", "title": "prepare annotation for Refseq", "topics": [ "PrepareAnnotationRefseq" ] }, { "page": "SharedJunc", "title": "Generate shared junctions dataset from multiple BED files", "topics": [ "SharedJunc" ] }, { "page": "Varlocation", "title": "Annotates the variations with genomic location.", "topics": [ "Varlocation" ] } ], "_rundeps": [ "abind", "AhoCorasickTrie", "AnnotationDbi", "askpass", "BH", "Biobase", "BiocFileCache", "BiocGenerics", "BiocIO", "BiocParallel", "biomaRt", "Biostrings", "bit", "bit64", "bitops", "blob", "BSgenome", "cachem", "cigarillo", "cli", "codetools", "cpp11", "crayon", "curl", "DBI", "dbplyr", "DelayedArray", "dplyr", "fastmap", "filelock", "formatR", "futile.logger", "futile.options", "generics", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "glue", "hms", "httr", "httr2", "IRanges", "jsonlite", "KEGGREST", "lambda.r", "lattice", "lifecycle", 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