Package Recipe 'bioconductor-infercnv'

recipe bioconductor-infercnv

Infer Copy Number Variation from Single-Cell RNA-Seq Data

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/infercnv.html
License:: BSD_3_clause + file LICENSE
Recipe:: /bioconductor-infercnv/meta.yaml

Using single-cell RNA-Seq expression to visualize CNV in cells.

package bioconductor-infercnv¶

Versions:

1.26.0-0, 1.22.0-0, 1.20.0-0, 1.18.1-1, 1.18.1-0, 1.16.0-0, 1.14.0-0, 1.10.0-0, 1.8.0-0,

1.26.0-0, 1.22.0-0, 1.20.0-0, 1.18.1-1, 1.18.1-0, 1.16.0-0, 1.14.0-0, 1.10.0-0, 1.8.0-0, 1.6.0-1, 1.6.0-0, 1.4.0-0, 1.2.0-0, 1.0.3-0

Depends:

on bioconductor-biocgenerics >=0.56.0,<0.57.0
on bioconductor-edger >=4.8.0,<4.9.0
on bioconductor-singlecellexperiment >=1.32.0,<1.33.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on jags
on r-ape
on r-argparse
on r-base >=4.5,<4.6.0a0
on r-catools
on r-coda
on r-coin
on r-digest
on r-doparallel
on r-dplyr
on r-fastcluster
on r-fitdistrplus
on r-foreach
on r-futile.logger
on r-future
on r-ggplot2
on r-gplots
on r-gridextra
on r-hiddenmarkov
on r-igraph
on r-matrix
on r-paralleldist
on r-phyclust
on r-rann
on r-rcolorbrewer
on r-reshape2
on r-rjags
on r-seurat
on r-tidyr

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-infercnv

to add into an existing workspace instead, run:

pixi add bioconductor-infercnv

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-infercnv

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-infercnv

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

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

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

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-infercnv/README.html)