recipe bioconductor-artms

artMS provides a set of tools for the analysis of proteomics label-free datasets. It takes as input the MaxQuant search result output (evidence.txt file) and performs quality control, relative quantification using MSstats, downstream analysis and integration. artMS also provides a set of functions to re-format and make it compatible with other analytical tools, including, SAINTq, SAINTexpress, Phosfate, and PHOTON. Check [http://artms.org](http://artms.org) for details.

Homepage

https://bioconductor.org/packages/3.9/bioc/html/artMS.html

License

GPL (>= 3) + file LICENSE

Recipe

/bioconductor-artms/meta.yaml

package bioconductor-artms

(downloads) docker_bioconductor-artms

Versions

1.0.10-0, 1.0.1-0

Depends bioconductor-annotationdbi

>=1.44.0,<1.45.0

Depends bioconductor-biomart

>=2.38.0,<2.39.0

Depends bioconductor-complexheatmap

>=1.20.0,<1.21.0

Depends bioconductor-limma

>=3.38.0,<3.39.0

Depends bioconductor-msstats

>=3.14.0,<3.15.0

Depends bioconductor-org.hs.eg.db

>=3.7.0,<3.8.0

Depends bioconductor-org.mm.eg.db

>=3.7.0,<3.8.0

Depends r-base

>=3.5.1,<3.5.2.0a0

Depends r-bit64

Depends r-circlize

Depends r-cluster

Depends r-corrplot

Depends r-data.table

Depends r-dplyr

Depends r-factoextra

Depends r-factominer

Depends r-getopt

Depends r-ggdendro

Depends r-ggplot2

Depends r-ggrepel

Depends r-gplots

Depends r-gprofiler

Depends r-openxlsx

Depends r-performanceanalytics

Depends r-pheatmap

Depends r-plotly

Depends r-plyr

Depends r-rcolorbrewer

Depends r-reshape2

Depends r-seqinr

Depends r-stringr

Depends r-tidyr

Depends r-upsetr

Depends r-venndiagram

Depends r-yaml

Requirements

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-artms

and update with:

conda update bioconductor-artms

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-artms:<tag>

(see bioconductor-artms/tags for valid values for <tag>)