recipe bioconductor-tbsignatureprofiler

Profile RNA-Seq Data Using TB Pathway Signatures

Homepage:

https://bioconductor.org/packages/3.16/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:

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

Depends:

• bioconductor-assign >=1.34.0,<1.35.0

• bioconductor-biocgenerics >=0.44.0,<0.45.0

• bioconductor-biocparallel >=1.32.0,<1.33.0

• bioconductor-complexheatmap >=2.14.0,<2.15.0

• bioconductor-deseq2 >=1.38.0,<1.39.0

• bioconductor-edger >=3.40.0,<3.41.0

• bioconductor-gsva >=1.46.0,<1.47.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• bioconductor-singscore >=1.18.0,<1.19.0

• bioconductor-summarizedexperiment >=1.28.0,<1.29.0

• r-base >=4.2,<4.3.0a0

• r-dt

• r-gdata

• r-ggplot2

• r-magrittr

• r-rcolorbrewer

• r-reshape2

• r-rlang

• r-rocit

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-tbsignatureprofiler

and update with:

conda update bioconductor-tbsignatureprofiler

or use the docker container:

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

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

Download stats

Link to this page

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