Doscheda
This is the released version of Doscheda; for the devel version, see Doscheda.
A DownStream Chemo-Proteomics Analysis Pipeline
Bioconductor version: Release (3.23)
Doscheda focuses on quantitative chemoproteomics used to determine protein interaction profiles of small molecules from whole cell or tissue lysates using Mass Spectrometry data. The package provides a shiny application to run the pipeline, several visualisations and a downloadable report of an experiment.
Author: Bruno Contrino, Piero Ricchiuto
Maintainer: Bruno Contrino <br1contrino at yahoo.co.uk>
citation("Doscheda")):
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("Doscheda")
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("Doscheda")| Doscheda | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataImport, MassSpectrometry, Normalization, Preprocessing, Proteomics, QualityControl, Regression, Software |
| Version | 1.34.0 |
| In Bioconductor since | BioC 3.6 (R-3.4) (9 years) |
| License | GPL-3 |
| Depends | R (>= 3.4) |
| Imports | methods, drc, stats, httr, jsonlite, reshape2, vsn, affy, limma, stringr, ggplot2, graphics, grDevices, calibrate, corrgram, gridExtra, DT, shiny, shinydashboard, readxl, prodlim, matrixStats |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle, knitr, rmarkdown, testthat |
| 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 | Doscheda_1.34.0.tar.gz |
| Windows Binary (x86_64) | Doscheda_1.34.0.zip |
| macOS Binary (big-sur-x86_64) | Doscheda_1.34.0.tgz |
| macOS Binary (sonoma-arm64) | Doscheda_1.34.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/Doscheda |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/Doscheda |
| Bioc Package Browser | https://code.bioconductor.org/browse/Doscheda/ |
| Package Short Url | https://bioconductor.org/packages/Doscheda/ |
| Package Downloads Report | Download Stats |