recipe bioconductor-artms

Analytical R tools for Mass Spectrometry

Homepage:

https://bioconductor.org/packages/3.18/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:

1.20.0-0,  1.18.0-0,  1.16.0-0,  1.12.0-0,  1.10.0-0,  1.8.2-0,  1.8.0-0,  1.6.3-0,  1.4.0-0, 

1.20.0-0,  1.18.0-0,  1.16.0-0,  1.12.0-0,  1.10.0-0,  1.8.2-0,  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:

>=1.64.0,<1.65.0

depends bioconductor-limma:

>=3.58.0,<3.59.0

depends bioconductor-msstats:

>=4.10.0,<4.11.0

depends bioconductor-org.hs.eg.db:

>=3.18.0,<3.19.0

depends r-base:

>=4.3,<4.4.0a0

depends r-bit64:

depends r-circlize:

depends r-cluster:

depends r-corrplot:

depends r-data.table:

depends r-dplyr:

depends r-getopt:

depends r-ggdendro:

depends r-ggplot2:

depends r-ggrepel:

depends r-gplots:

depends r-openxlsx:

depends r-pheatmap:

depends r-plotly:

depends r-plyr:

depends r-rcolorbrewer:

depends r-scales:

depends r-seqinr:

depends r-stringr:

depends r-tidyr:

depends r-upsetr:

depends r-venndiagram:

depends r-yaml:

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-artms

and update with::

   mamba update bioconductor-artms

To create a new environment, run:

mamba create --name myenvname bioconductor-artms

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

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

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

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