recipe bioconductor-scmerge

scMerge: Merging multiple batches of scRNA-seq data

Homepage

https://bioconductor.org/packages/3.11/bioc/html/scMerge.html

License

GPL-3

Recipe

/bioconductor-scmerge/meta.yaml

Like all gene expression data, single-cell RNA-seq (scRNA-Seq) 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 scRNA-Seq data. This package contains all the necessary functions in the scMerge pipeline, including the identification of SEGs, replication-identification methods, and merging of scRNA-Seq data.

package bioconductor-scmerge

Versions

1.4.0-0,  1.2.0-0,  1.0.0-1

Depends

• bioconductor-biocparallel >=1.22.0,<1.23.0

• bioconductor-biocsingular >=1.4.0,<1.5.0

• bioconductor-delayedarray >=0.14.0,<0.15.0

• bioconductor-delayedmatrixstats >=1.10.0,<1.11.0

• bioconductor-m3drop >=1.14.0,<1.15.0

• bioconductor-s4vectors >=0.26.0,<0.27.0

• bioconductor-singlecellexperiment >=1.10.0,<1.11.0

• bioconductor-summarizedexperiment >=1.18.0,<1.19.0

• libblas >=3.8.0,<4.0a0

• libgcc-ng >=7.3.0

• liblapack >=3.8.0,<3.9.0a0

• libstdcxx-ng >=7.3.0

• r-base >=4.0,<4.1.0a0

• r-cluster

• r-distr

• r-dplyr

• r-igraph

• r-pdist

• r-proxy

• r-rcpp >=0.12.18

• r-rcppeigen >=0.3.3.4.0

• r-ruv

• r-testthat

Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-scmerge

and update with:

conda update bioconductor-scmerge

or use the docker container:

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

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

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)