recipe bioconductor-tbsignatureprofiler

Profile RNA-Seq Data Using TB Pathway Signatures

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/TBSignatureProfiler.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-tbsignatureprofiler/meta.yaml

Gene signatures of TB progression, TB disease, and other TB disease states have been validated and published previously. This package aggregates known signatures and provides computational tools to enlist their usage on other datasets. The TBSignatureProfiler makes it easy to profile RNA-Seq data using these signatures and includes common signature profiling tools including ASSIGN, GSVA, and ssGSEA. Original models for some gene signatures are also available. A shiny app provides some functionality alongside for detailed command line accessibility.

package bioconductor-tbsignatureprofiler

versions:

1.14.0-0,  1.12.0-0,  1.10.0-0,  1.6.0-0,  1.2.0-1,  1.2.0-0,  1.0.0-0

depends bioconductor-assign:

>=1.38.0,<1.39.0

depends bioconductor-biocparallel:

>=1.36.0,<1.37.0

depends bioconductor-complexheatmap:

>=2.18.0,<2.19.0

depends bioconductor-deseq2:

>=1.42.0,<1.43.0

depends bioconductor-edger:

>=4.0.0,<4.1.0

depends bioconductor-gsva:

>=1.50.0,<1.51.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-singscore:

>=1.22.0,<1.23.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-base:

>=4.3,<4.4.0a0

depends r-dt:

depends r-gdata:

depends r-ggplot2:

depends r-magrittr:

depends r-rcolorbrewer:

depends r-reshape2:

depends r-rlang:

depends r-rocit:

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-tbsignatureprofiler

and update with::

   mamba update bioconductor-tbsignatureprofiler

To create a new environment, run:

mamba create --name myenvname bioconductor-tbsignatureprofiler

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-tbsignatureprofiler:<tag>

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

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Link to this page

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