Package Recipe 'bioconductor-scmerge'

recipe bioconductor-scmerge

scMerge: Merging multiple batches of scRNA-seq data

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

Like all gene expression data, single-cell data suffers from batch effects and other unwanted variations that makes accurate biological interpretations difficult. The scMerge method leverages factor analysis, stably expressed genes (SEGs) and (pseudo-) replicates to remove unwanted variations and merge multiple single-cell data. This package contains all the necessary functions in the scMerge pipeline, including the identification of SEGs, replication-identification methods, and merging of single-cell data.

package bioconductor-scmerge¶

Versions:

1.26.0-0, 1.22.0-0, 1.18.0-0, 1.16.0-0, 1.14.0-0, 1.10.0-0, 1.8.0-0, 1.6.0-1, 1.6.0-0,

1.26.0-0, 1.22.0-0, 1.18.0-0, 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, 1.0.0-1

Depends:

on bioconductor-batchelor >=1.26.0,<1.27.0
on bioconductor-biocneighbors >=2.4.0,<2.5.0
on bioconductor-biocparallel >=1.44.0,<1.45.0
on bioconductor-biocsingular >=1.26.0,<1.27.0
on bioconductor-delayedarray >=0.36.0,<0.37.0
on bioconductor-delayedmatrixstats >=1.32.0,<1.33.0
on bioconductor-m3drop >=1.36.0,<1.37.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-scater >=1.38.0,<1.39.0
on bioconductor-scran >=1.38.0,<1.39.0
on bioconductor-singlecellexperiment >=1.32.0,<1.33.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on r-base >=4.5,<4.6.0a0
on r-cluster
on r-cvtools
on r-distr
on r-igraph
on r-proxyc
on r-ruv

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-scmerge

to add into an existing workspace instead, run:

pixi add bioconductor-scmerge

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-scmerge

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-scmerge

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-scmerge:<tag>

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