Doscheda

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see Doscheda.

A DownStream Chemo-Proteomics Analysis Pipeline

Bioconductor version: 3.14

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 "4.1") 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 PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

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

Version 1.16.0

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

URL

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_1.16.0.tar.gz

Windows Binary Doscheda_1.16.0.zip

macOS 10.13 (High Sierra) Doscheda_1.16.0.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

Old Source Packages for BioC 3.14 Source Archive