ProteoDisco

This is the released version of ProteoDisco; for the devel version, see ProteoDisco.

Generation of customized protein variant databases from genomic variants, splice-junctions and manual sequences

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DOI: 10.18129/B9.bioc.ProteoDisco

Bioconductor version: Release (3.22)

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")):

Installation

To install this package, start R (version "4.5") 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.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("ProteoDisco")

Overview_Proteodisco HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DataImport, Proteomics, RNASeq, SNP, Sequencing, Software, VariantAnnotation

Version 1.16.0

In Bioconductor since BioC 3.14 (R-4.1) (4 years)

License GPL-3

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)

System Requirements

URL https://github.com/ErasmusMC-CCBC/ProteoDisco

Bug Reports https://github.com/ErasmusMC-CCBC/ProteoDisco/issues