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ProteoDisco
This is thereleased version of ProteoDisco; for the devel version, seeProteoDisco.
Generation of customized protein variant databases from genomic variants, splice-junctions and manual sequences
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("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 appropriateBioconductor 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 | 1.16.0 |
| 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 |
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
FollowInstallation instructions to use this package in your R session.
| Source Package | ProteoDisco_1.16.0.tar.gz |
| Windows Binary (x86_64) | ProteoDisco_1.16.0.zip |
| macOS Binary (x86_64) | ProteoDisco_1.16.0.tgz |
| macOS Binary (arm64) | ProteoDisco_1.16.0.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 |