recipe bioconductor-quantiseqr

Quantification of the Tumor Immune contexture from RNA-seq data

Homepage

https://bioconductor.org/packages/3.14/bioc/html/quantiseqr.html

License

GPL-3

Recipe

/bioconductor-quantiseqr/meta.yaml

This package provides a streamlined workflow for the quanTIseq method, developed to perform the quantification of the Tumor Immune contexture from RNA-seq data. The quantification is performed against the TIL10 signature (dissecting the contributions of ten immune cell types), carefully crafted from a collection of human RNA-seq samples. The TIL10 signature has been extensively validated using simulated, flow cytometry, and immunohistochemistry data.

package bioconductor-quantiseqr

Versions

1.2.0-0,  1.0.0-0

Depends

• bioconductor-biobase >=2.54.0,<2.55.0

• bioconductor-preprocesscore >=1.56.0,<1.57.0

• bioconductor-summarizedexperiment >=1.24.0,<1.25.0

• r-base >=4.1,<4.2.0a0

• r-ggplot2

• r-limsolve

• r-mass

• r-rlang

• r-tidyr

Required By

• bioconductor-easier

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-quantiseqr

and update with:

conda update bioconductor-quantiseqr

or use the docker container:

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

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

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-quantiseqr/README.html)