recipe bioconductor-partcnv

Infer locally aneuploid cells using single cell RNA-seq data

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/partCNV.html

License:

GPL-2

Recipe:

/bioconductor-partcnv/meta.yaml

This package uses a statistical framework for rapid and accurate detection of aneuploid cells with local copy number deletion or amplification. Our method uses an EM algorithm with mixtures of Poisson distributions while incorporating cytogenetics information (e.g., regional deletion or amplification) to guide the classification (partCNV). When applicable, we further improve the accuracy by integrating a Hidden Markov Model for feature selection (partCNVH).

package bioconductor-partcnv

versions:

1.0.0-0

depends bioconductor-annotationhub:

>=3.10.0,<3.11.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-singlecellexperiment:

>=1.24.0,<1.25.0

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

depends r-depmixs4:

depends r-magrittr:

depends r-seurat:

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 bioconductor-partcnv

and update with::

   mamba update bioconductor-partcnv

To create a new environment, run:

mamba create --name myenvname bioconductor-partcnv

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/bioconductor-partcnv:<tag>

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

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Link to this page

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[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-partcnv/README.html)