Package Recipe 'bioconductor-artms'

recipe bioconductor-artms

Analytical R tools for Mass Spectrometry

Homepage:: https://bioconductor.org/packages/3.20/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:

1.28.0-0, 1.24.0-0, 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,

1.28.0-0, 1.24.0-0, 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:

on bioconductor-annotationdbi >=1.72.0,<1.73.0
on bioconductor-limma >=3.66.0,<3.67.0
on bioconductor-msstats >=4.18.0,<4.19.0
on bioconductor-org.hs.eg.db >=3.22.0,<3.23.0
on r-base >=4.5,<4.6.0a0
on r-bit64
on r-circlize
on r-cluster
on r-corrplot
on r-data.table
on r-dplyr
on r-getopt
on r-ggdendro
on r-ggplot2
on r-ggrepel
on r-gplots
on r-openxlsx
on r-pheatmap
on r-plotly
on r-plyr
on r-rcolorbrewer
on r-scales
on r-seqinr
on r-stringr
on r-tidyr
on r-upsetr
on r-venndiagram
on r-yaml

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-artms

to add into an existing workspace instead, run:

pixi add bioconductor-artms

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-artms

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-artms

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

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

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

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)