description

MCQR is an R package dedicated to statistical analysis of proteomic data. The goal of the MCQR is to provide a consistent set of functions facilitating proteomics data statistical analysis. It can be used without extensive programming knowledge with R.

help and support

MCQR is developped by the PAPPSO team. We are providing support through our mailing list. Don't hesitate to register if you want to be informed of new releases or upgrades. The development is open and free, you are welcome to contribute, copy, modify, fork if you need it, respecting the terms of the licence.

download and install

All downloadable files concerning MCQR 0.4.4 can be found at SourceSup.

Under Windows

To install this package, launch R (version >= 3.1) and execute these R commands :

#Install required package from bioconductor :
source("https://bioconductor.org/biocLite.R")
biocLite("made4")

#Install required modules :
install.packages(pkgs=c('zoo','mvtnorm','XML','multcomp','bitops','caTools', 'gplots','gtools','gdata','chron','stringi','stringr','reshape2', 'data.table','readODS','vcd','lme4','car','robustbase','colorspace','VIM', 'ade4','clValid','agricolae','ggplot2','gridExtra','Hmisc', 'RColorBrewer' ,'plotly', 'plyr', 'dplyr'))

#temporarily install the unstable R agricolae 1.2.9
install.packages('http://pappso.inra.fr/downloads/masschroqr/agricolae_1.2-9.tar.gz',repos = NULL, type = 'source')

#Install MCQR
install.packages('https://sourcesup.renater.fr/frs/download.php/latestfile/2225/MCQR_0.4.4.tar.gz', repos = NULL, type = 'source')

Under Debian 10 or Ubuntu 18.04

Install the following required packages in a terminal :

sudo apt update
sudo apt install r-base wget curl liblapack-dev libxml2-dev libblas-dev libcurl4-openssl-dev r-cran-nloptr r-cran-xml r-cran-xml2 r-cran-mvtnorm r-cran-multcomp r-cran-bitops r-cran-catools r-cran-gtools r-cran-gdata r-cran-chron r-cran-stringi r-cran-stringr r-cran-reshape2 r-cran-data.table r-cran-vcd r-cran-lme4 r-cran-car r-cran-robustbase r-cran-colorspace r-cran-ade4 r-cran-gplots r-cran-ggplot2 r-cran-gridextra r-cran-hmisc r-cran-rcolorbrewer r-cran-mgcv r-cran-plyr r-cran-dplyr r-cran-plotly

Launch R (version >= 3.5) and execute these R commands :

#Install required package from bioconductor :
source("https://bioconductor.org/biocLite.R")
biocLite("made4")

#Install required modules :
install.packages(pkgs=c('readODS','VIM','clValid','agricolae'))

#Install MCQR
install.packages('https://sourcesup.renater.fr/frs/download.php/latestfile/2225/MCQR_0.4.4.tar.gz', repos = NULL, type = 'source')

Annotated script

MCQR comes with an annotated script available here and for SDS-PAGE here

licence

MCQR is a free software distributed under the terms of the GNU GENERAL PUBLIC licence v3.

contribute

The source code of MCQR is hosted by SourceSup. Contributors are welcome to send bug reports or directly access to the git repository via SourceSup registration.