Package: ProteoDisco
Type: Package
Title: Generation of customized protein variant databases from genomic variants, splice-junctions and manual sequences
Version: 1.17.0
Date: 2025-07-22
Authors@R: c(
    person("Job", "van Riet", email = "jobvriet@gmail.com", role = c("cre")),
    person("Wesley", "van de Geer", email = "w.vandegeer@erasmusmc.nl", role = c("aut")),
    person("Harmen", "van de Werken", email = "h.vandewerken@erasmusmc.nl", role = c("ths")))
biocViews: Software, Proteomics, RNASeq, SNP, Sequencing, VariantAnnotation, DataImport
URL: https://github.com/ErasmusMC-CCBC/ProteoDisco
BugReports: https://github.com/ErasmusMC-CCBC/ProteoDisco/issues
Description: ProteoDisco is an R package to facilitate proteogenomics studies. 
    It houses functions to create customized (variant) protein databases based on user-submitted genomic variants, splice-junctions, fusion genes and manual transcript sequences.
    The flexible workflow can be adopted to suit a myriad of research and experimental settings.
License: GPL-3
LazyData: FALSE
Depends:
    R (>= 4.1.0),
Imports:
    BiocGenerics (>= 0.38.0),
    BiocParallel (>= 1.26.0),
    Biostrings (>= 2.60.1),
    checkmate (>= 2.0.0),
    cleaver (>= 1.30.0),
    dplyr (>= 1.0.6),
    GenomeInfoDb (>= 1.28.0),
    GenomicFeatures (>= 1.44.0),
    GenomicRanges (>= 1.44.0),
    IRanges (>= 2.26.0),
    methods (>= 4.1.0),
    ParallelLogger (>= 2.0.1),
    plyr (>= 1.8.6),
    rlang (>= 0.4.11),
    S4Vectors (>= 0.30.0),
    Seqinfo,
    tibble (>= 3.1.2),
    tidyr (>= 1.1.3),
    VariantAnnotation (>= 1.36.0),
    XVector (>= 0.32.0),
RoxygenNote: 7.1.2
Suggests: 
    AnnotationDbi (>= 1.54.1),
    BSgenome (>= 1.60.0),
    BSgenome.Hsapiens.UCSC.hg19 (>= 1.4.3),
    BiocStyle (>= 2.20.1),
    DelayedArray (>= 0.18.0),
    devtools (>= 2.4.2),
    knitr (>= 1.33),
    matrixStats (>= 0.59.0),
    markdown (>= 1.1),
    org.Hs.eg.db (>= 3.13.0),
    purrr (>= 0.3.4),
    RCurl (>= 1.98.1.3),
    readr (>= 1.4.0),
    ggplot2 (>= 3.3.5),
    rmarkdown (>= 2.9),
    rtracklayer (>= 1.52.0),
    seqinr (>= 4.2.8),
    stringr (>= 1.4.0),
    reshape2 (>= 1.4.4),
    scales (>= 1.1.1),
    testthat (>= 3.0.3),
    TxDb.Hsapiens.UCSC.hg19.knownGene (>= 3.2.2)
VignetteBuilder: knitr
Encoding: UTF-8
git_url: https://git.bioconductor.org/packages/ProteoDisco
git_branch: devel
git_last_commit: 583baa5
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
