Package Recipe 'bioconductor-mitoclone2'

recipe bioconductor-mitoclone2

Clonal Population Identification in Single-Cell RNA-Seq Data using Mitochondrial and Somatic Mutations

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/mitoClone2.html
License:: GPL-3
Recipe:: /bioconductor-mitoclone2/meta.yaml

This package primarily identifies variants in mitochondrial genomes from BAM alignment files. It filters these variants to remove RNA editing events then estimates their evolutionary relationship (i.e. their phylogenetic tree) and groups single cells into clones. It also visualizes the mutations and providing additional genomic context.

package bioconductor-mitoclone2¶

Versions:

1.16.0-0, 1.12.0-0, 1.8.1-0, 1.6.0-0, 1.4.0-1, 1.4.0-0, 1.0.0-2, 1.0.0-1, 1.0.0-0

Depends:

on bioconductor-deepsnv >=1.56.0,<1.57.0
on bioconductor-deepsnv >=1.56.0,<1.57.0a0
on bioconductor-genomicranges >=1.62.0,<1.63.0
on bioconductor-genomicranges >=1.62.1,<1.63.0a0
on bioconductor-rhtslib >=3.6.0,<3.7.0
on bioconductor-rhtslib >=3.6.0,<3.7.0a0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-s4vectors >=0.48.0,<0.49.0a0
on libblas >=3.9.0,<4.0a0
on libgcc >=14
on liblapack >=3.9.0,<4.0a0
on liblzma >=5.8.2,<6.0a0
on libstdcxx >=14
on libzlib >=1.3.1,<2.0a0
on r-base >=4.5,<4.6.0a0
on r-ggplot2
on r-matrix
on r-pheatmap
on r-reshape2

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-mitoclone2

to add into an existing workspace instead, run:

pixi add bioconductor-mitoclone2

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-mitoclone2

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-mitoclone2

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-mitoclone2:<tag>

(see bioconductor-mitoclone2/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-mitoclone2/README.html)