Doscheda

This is the development version of Doscheda; for the stable release version, see Doscheda.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6

A DownStream Chemo-Proteomics Analysis Pipeline

Bioconductor version: Development (3.24)

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 (from within R, enter citation("Doscheda")):

Bruno Contrino, Piero Ricchiuto. Doscheda: A DownStream Chemo-Proteomics Analysis Pipeline. doi:10.18129/B9.bioc.Doscheda, R package version 1.35.0, https://bioconductor.org/packages/Doscheda.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, MassSpectrometry, Normalization, Preprocessing, Proteomics, QualityControl, Regression, Software
Version	1.35.0
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

Suggests	BiocStyle, knitr, rmarkdown, testthat
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	Doscheda_1.35.0.tar.gz
Windows Binary (x86_64)	Doscheda_1.35.0.zip
macOS Binary (big-sur-x86_64)	Doscheda_1.35.0.tgz
macOS Binary (sonoma-arm64)	Doscheda_1.35.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/Doscheda
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/Doscheda
Package Short Url	https://bioconductor.org/packages/Doscheda/
Package Downloads Report	Download Stats