recipe bioconductor-artms

Analytical R tools for Mass Spectrometry

Homepage

https://bioconductor.org/packages/3.12/bioc/html/artMS.html

License

GPL (>= 3) + file LICENSE

Recipe

/bioconductor-artms/meta.yaml

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.

package bioconductor-artms

Versions

1.8.0-0,  1.6.3-0,  1.4.0-0,  1.2.6-0,  1.0.10-0,  1.0.1-0

Depends

• bioconductor-annotationdbi >=1.52.0,<1.53.0

• bioconductor-biomart >=2.46.0,<2.47.0

• bioconductor-complexheatmap >=2.6.0,<2.7.0

• bioconductor-limma >=3.46.0,<3.47.0

• bioconductor-msstats >=3.22.0,<3.23.0

• bioconductor-org.hs.eg.db >=3.12.0,<3.13.0

• bioconductor-org.mm.eg.db >=3.12.0,<3.13.0

• r-base >=4.0,<4.1.0a0

• r-bit64

• r-circlize

• r-cluster

• r-corrplot

• r-data.table

• r-dplyr

• r-factoextra

• r-factominer

• r-getopt

• r-ggdendro

• r-ggplot2

• r-ggrepel

• r-gplots

• r-gprofiler

• r-openxlsx

• r-performanceanalytics

• r-pheatmap

• r-plotly

• r-plyr

• r-rcolorbrewer

• r-scales

• r-seqinr

• r-stringr

• r-tidyr

• r-upsetr

• r-venndiagram

• r-yaml

Required By

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>)

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-artms/README.html)