ProteoDisco
This is the released version of ProteoDisco; for the devel version, see ProteoDisco.
All Bioconductor versions of ProteoDisco
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14
Generation of customized protein variant databases from genomic variants, splice-junctions and manual sequences
Bioconductor version: 3.23 · Package version: 1.18.0
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.
Author: Job van Riet [cre], Wesley van de Geer [aut], Harmen van de Werken [ths]
Maintainer: Job van Riet <jobvriet at gmail.com>
Citation
From within R, enter citation("ProteoDisco"):
Wesley van de Geer. ProteoDisco: Generation of customized protein variant databases from genomic variants, splice-junctions and manual sequences. doi:10.18129/B9.bioc.ProteoDisco, R package version 1.18.0, https://bioconductor.org/packages/ProteoDisco.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ProteoDisco")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.18.0 |
| License | GPL-3 |
| URL | https://github.com/ErasmusMC-CCBC/ProteoDisco |
| Bug Reports | https://github.com/ErasmusMC-CCBC/ProteoDisco/issues |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.14 (R-4.1) (4 years) |
| Downloads rank | 1162 of 2,418 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | DataImport, Proteomics, RNASeq, SNP, Sequencing, Software, VariantAnnotation |
| Package Short Url | https://bioconductor.org/packages/ProteoDisco/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("ProteoDisco")| Overview of Proteodisco | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | ProteoDisco_1.18.0.tar.gz |
| Windows binary (x86_64) | ProteoDisco_1.18.0.zip |
| macOS binary (arm64) | ProteoDisco_1.18.0.tgz |
| macOS binary (x86_64) | ProteoDisco_1.18.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ProteoDisco |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ProteoDisco |
| Package Downloads Report | Download Stats |
Dependencies
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)
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)