ProteoDisco
This package is for version 3.16 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: 3.16
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("ProteoDisco")):
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")| Overview_Proteodisco | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataImport, Proteomics, RNASeq, SNP, Sequencing, Software, VariantAnnotation |
| Version | 1.4.0 |
| In Bioconductor since | BioC 3.14 (R-4.1) (2.5 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), 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 |
See More
| 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) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | ProteoDisco_1.4.0.tar.gz |
| Windows Binary | ProteoDisco_1.4.0.zip |
| macOS Binary (x86_64) | ProteoDisco_1.4.0.tgz |
| macOS Binary (arm64) | ProteoDisco_1.4.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ProteoDisco |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ProteoDisco |
| Bioc Package Browser | https://code.bioconductor.org/browse/ProteoDisco/ |
| Package Short Url | https://bioconductor.org/packages/ProteoDisco/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.16 | Source Archive |