Package: ProteoDisco
Type: Package
Title: Generation of customized protein variant databases from genomic
        variants, splice-junctions and manual sequences
Version: 1.19.0
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
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 12:56:49 UTC
RemoteUrl: https://github.com/bioc/ProteoDisco
RemoteRef: HEAD
RemoteSha: 13dc81426f0936e97284f28fdb852c2f7c9d081c
NeedsCompilation: no
Packaged: 2026-07-04 23:31:03 UTC; root
Author: Job van Riet [cre],
  Wesley van de Geer [aut],
  Harmen van de Werken [ths]
Maintainer: Job van Riet <jobvriet@gmail.com>