ComPrAn
This is the released version of ComPrAn; for the devel version, see ComPrAn.
Complexome Profiling Analysis package
Bioconductor version: Release (3.23)
This package is for analysis of SILAC labeled complexome profiling data. It uses peptide table in tab-delimited format as an input and produces ready-to-use tables and plots.
Author: Rick Scavetta [aut], Petra Palenikova [aut, cre]
Maintainer: Petra Palenikova <palenikova3 at gmail.com>
citation("ComPrAn")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ComPrAn")
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("ComPrAn")| fileFormats.html | HTML | R Script |
| Protein workflow | HTML | R Script |
| SILAC complexomics | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | MassSpectrometry, Proteomics, Software, Visualization |
| Version | 1.20.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (5 years) |
| License | MIT + file LICENSE |
| Depends | |
| Imports | data.table, dplyr, forcats, ggplot2, magrittr, purrr, tidyr, rlang, stringr, shiny, DT, RColorBrewer, VennDiagram, rio, scales, shinydashboard, shinyjs, stats, tibble, grid |
| System Requirements | |
| URL |
See More
| Suggests | testthat (>= 2.1.0), knitr, rmarkdown |
| 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 | ComPrAn_1.20.0.tar.gz |
| Windows Binary (x86_64) | ComPrAn_1.20.0.zip |
| macOS Binary (big-sur-x86_64) | ComPrAn_1.20.0.tgz |
| macOS Binary (sonoma-arm64) | ComPrAn_1.20.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ComPrAn |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ComPrAn |
| Bioc Package Browser | https://code.bioconductor.org/browse/ComPrAn/ |
| Package Short Url | https://bioconductor.org/packages/ComPrAn/ |
| Package Downloads Report | Download Stats |