recipe bioconductor-quantiseqr

Quantification of the Tumor Immune contexture from RNA-seq data

Homepage:

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

1.6.0-0,  1.2.0-0,  1.0.0-0

Depends:

• bioconductor-biobase >=2.58.0,<2.59.0

• bioconductor-preprocesscore >=1.60.0,<1.61.0

• bioconductor-summarizedexperiment >=1.28.0,<1.29.0

• r-base >=4.2,<4.3.0a0

• r-ggplot2

• r-limsolve

• r-mass

• r-rlang

• r-tidyr

Required By:

• r-immunedeconv

• bioconductor-easier

Installation

With an activated Bioconda channel (see 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

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