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Doscheda

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

A DownStream Chemo-Proteomics Analysis Pipeline


Bioconductor version: Development (3.19)

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")):

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
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

Details

biocViews DataImport, MassSpectrometry, Normalization, Preprocessing, Proteomics, QualityControl, Regression, Software
Version 1.25.0
In Bioconductor since BioC 3.6 (R-3.4) (6.5 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
System Requirements
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Suggests BiocStyle, knitr, rmarkdown, testthat
Linking To
Enhances
Depends On Me
Imports Me
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Build Report Build Report

Package Archives

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

Source Package Doscheda_1.25.0.tar.gz
Windows Binary Doscheda_1.25.0.zip (64-bit only)
macOS Binary (x86_64) Doscheda_1.25.0.tgz
macOS Binary (arm64) Doscheda_1.25.0.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