ProteoDisco

DOI: 10.18129/B9.bioc.ProteoDisco    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see ProteoDisco.

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

Bioconductor version: 3.15

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>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	Overview_Proteodisco
PDF		Reference Manual
Text		NEWS

Details

biocViews	DataImport, Proteomics, RNASeq, SNP, Sequencing, Software, VariantAnnotation
Version	1.2.0
In Bioconductor since	BioC 3.14 (R-4.1) (1 year)
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), tibble (>= 3.1.2), tidyr (>= 1.1.3), VariantAnnotation(>= 1.36.0), XVector(>= 0.32.0)
LinkingTo
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)
SystemRequirements
Enhances
URL	https://github.com/ErasmusMC-CCBC/ProteoDisco
BugReports	https://github.com/ErasmusMC-CCBC/ProteoDisco/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	ProteoDisco_1.2.0.tar.gz
Windows Binary	ProteoDisco_1.2.0.zip
macOS Binary (x86_64)	ProteoDisco_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ProteoDisco
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ProteoDisco
Package Short Url	https://bioconductor.org/packages/ProteoDisco/
Package Downloads Report	Download Stats