recipe r-xcell

Estimate immune cell proportions from gene expression data

Homepage:

https://github.com/dviraran/xCell

License:

GPL / GPL-3

Recipe:

/r-xcell/meta.yaml

Links:

doi: 10.1186/s13059-017-1349-1

"Tissues are a complex milieu consisting of numerous cell types. In cancer, understanding the cellular heterogeneity in the tumor microenvironment is an emerging field of research. Numerous methods have been published in recent years for the enumeration of cell subsets from tissue expression profiles. However, the available methods suffer from three major problems: inferring cell subset based on gene sets learned and verified from limited sources; displaying only partial portrayal of the full cellular heterogeneity; and insufficient validation in mixed tissues. The xCell package performs cell type enrichment analysis from gene expression data for 64 immune and stroma cell types. xCell is a gene signatures-based method learned from thousands of pure cell types from various sources. xCell applies a novel technique for reducing associations between closley related cell types. xCell signatures were validated using extensive in-silico simulations and also cytometry immunophenotyping, and were shown to outperform previous methods. xCell allows researchers to reliably portray the cellular heterogeneity landscape of tissue expression profiles."

package r-xcell

versions:

1.3-6,  1.3-5,  1.3-4,  1.3-3,  1.3-2,  1.3-1,  1.3-0,  1.2-3,  1.2-2, 

1.3-6,  1.3-5,  1.3-4,  1.3-3,  1.3-2,  1.3-1,  1.3-0,  1.2-3,  1.2-2,  1.2-1,  1.2-0

depends bioconductor-gseabase:

depends bioconductor-gsva:

depends libgcc-ng:

>=12

depends libstdcxx-ng:

>=12

depends r-base:

>=4.3,<4.4.0a0

depends r-curl:

depends r-digest:

depends r-mass:

depends r-pracma:

depends r-quadprog:

depends r-roxygen2:

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 r-xcell

and update with::

   mamba update r-xcell

To create a new environment, run:

mamba create --name myenvname r-xcell

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/r-xcell:<tag>

(see `r-xcell/tags`_ for valid values for ``<tag>``)

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