Package Recipe 'bioconductor-m3drop'

recipe bioconductor-m3drop

Michaelis-Menten Modelling of Dropouts in single-cell RNASeq

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/M3Drop.html
License:: GPL (>=2)
Recipe:: /bioconductor-m3drop/meta.yaml
Links:: biotools: m3drop, doi: 10.1002/1873-3468.12684

This package fits a model to the pattern of dropouts in single-cell RNASeq data. This model is used as a null to identify significantly variable (i.e. differentially expressed) genes for use in downstream analysis, such as clustering cells. Also includes an method for calculating exact Pearson residuals in UMI-tagged data using a library-size aware negative binomial model.

package bioconductor-m3drop¶

Versions:

1.36.0-0, 1.32.0-0, 1.28.0-1, 1.28.0-0, 1.26.0-0, 1.24.0-0, 1.20.0-0, 1.18.0-0, 1.16.0-1,

1.36.0-0, 1.32.0-0, 1.28.0-1, 1.28.0-0, 1.26.0-0, 1.24.0-0, 1.20.0-0, 1.18.0-0, 1.16.0-1, 1.16.0-0, 1.14.0-0, 1.12.0-0, 1.10.0-1, 1.10.0-0, 1.8.1-0, 1.6.0-0, 1.4.0-0, 1.2.0-0

Depends:

on bioconductor-scater >=1.38.0,<1.39.0
on r-base >=4.5,<4.6.0a0
on r-bbmle
on r-gplots
on r-hmisc
on r-irlba
on r-matrix
on r-matrixstats
on r-numderiv
on r-rcolorbrewer
on r-reldist
on r-statmod

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-m3drop

to add into an existing workspace instead, run:

pixi add bioconductor-m3drop

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-m3drop

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-m3drop

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-m3drop:<tag>

(see bioconductor-m3drop/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-m3drop/README.html)