Doscheda

DOI: 10.18129/B9.bioc.Doscheda  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see Doscheda.

A DownStream Chemo-Proteomics Analysis Pipeline

Bioconductor version: 3.16

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>

Installation

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

 

HTML	R Script	Doscheda
PDF		Reference Manual
Text		NEWS

Details

biocViews	DataImport, MassSpectrometry, Normalization, Preprocessing, Proteomics, QualityControl, Regression, Software
Version	1.20.0
In Bioconductor since	BioC 3.6 (R-3.4) (5.5 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
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, testthat
SystemRequirements
Enhances
URL
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	Doscheda_1.20.0.tar.gz
Windows Binary	Doscheda_1.20.0.zip
macOS Binary (x86_64)	Doscheda_1.20.0.tgz
macOS Binary (arm64)	Doscheda_1.20.0.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