recipe monopogen

Monopogen is an analysis package for SNV calling from single-cell sequencing datasets generated from single cell RNA 10x 5', 10x 3', single ATAC-seq technoloiges, scDNA-seq, etc.

Homepage:

https://github.com/KChen-lab/Monopogen

License:

GPL3 / GPL-3.0-or-later

Recipe:

/monopogen/meta.yaml

Links:

doi: 10.1038/s41587-023-01873-x

package monopogen

versions:

1.6.0-0,  1.5.0-1,  1.5.0-0,  1.1.0-0

depends bcftools:

depends beagle:

depends numpy:

>=1.19.5

depends openjdk:

depends pandas:

>=1.2.3

depends pillow:

>=8.2.0

depends pysam:

>=0.16.0.1

depends python:

>=3.6

depends r-base:

depends r-data.table:

depends r-e1071:

depends r-ggplot2:

depends samtools:

depends scipy:

>=1.6.3

depends tabix:

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 monopogen

and update with::

   mamba update monopogen

To create a new environment, run:

mamba create --name myenvname monopogen

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/monopogen:<tag>

(see `monopogen/tags`_ for valid values for ``<tag>``)

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