recipe bioconductor-quantiseqr

Quantification of the Tumor Immune contexture from RNA-seq data






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

(downloads) docker_bioconductor-quantiseqr



depends bioconductor-biobase:


depends bioconductor-preprocesscore:


depends bioconductor-summarizedexperiment:


depends r-base:


depends r-ggplot2:

depends r-limsolve:

depends r-mass:

depends r-rlang:

depends r-tidyr:



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-quantiseqr

and update with::

   mamba update bioconductor-quantiseqr

To create a new environment, run:

mamba create --name myenvname bioconductor-quantiseqr

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<tag>

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

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