Package Recipe 'bioconductor-mastr'

recipe bioconductor-mastr

Markers Automated Screening Tool in R

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/mastR.html
License:: MIT + file LICENSE
Recipe:: /bioconductor-mastr/meta.yaml

mastR is an R package designed for automated screening of signatures of interest for specific research questions. The package is developed for generating refined lists of signature genes from multiple group comparisons based on the results from edgeR and limma differential expression (DE) analysis workflow. It also takes into account the background noise of tissue-specificity, which is often ignored by other marker generation tools. This package is particularly useful for the identification of group markers in various biological and medical applications, including cancer research and developmental biology.

package bioconductor-mastr¶

Versions:

1.10.2-0, 1.6.0-0, 1.2.0-0, 1.0.0-0

Depends:

on bioconductor-annotationdbi >=1.72.0,<1.73.0
on bioconductor-biobase >=2.70.0,<2.71.0
on bioconductor-edger >=4.8.0,<4.9.0
on bioconductor-gseabase >=1.72.0,<1.73.0
on bioconductor-limma >=3.66.0,<3.67.0
on bioconductor-msigdb >=1.18.0,<1.19.0
on bioconductor-org.hs.eg.db >=3.22.0,<3.23.0
on bioconductor-singlecellexperiment >=1.32.0,<1.33.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on r-base >=4.5,<4.6.0a0
on r-dplyr
on r-ggplot2
on r-ggpubr
on r-matrix
on r-patchwork
on r-seuratobject >5.0.0
on r-tidyr

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-mastr

to add into an existing workspace instead, run:

pixi add bioconductor-mastr

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-mastr

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-mastr

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-mastr:<tag>

(see bioconductor-mastr/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-mastr/README.html)