recipe bioconductor-scmerge

scMerge: Merging multiple batches of scRNA-seq data

Homepage:

https://bioconductor.org/packages/3.16/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:

1.14.0-0,  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:

• bioconductor-biocparallel >=1.32.0,<1.33.0

• bioconductor-biocsingular >=1.14.0,<1.15.0

• bioconductor-delayedarray >=0.24.0,<0.25.0

• bioconductor-delayedmatrixstats >=1.20.0,<1.21.0

• bioconductor-m3drop >=1.24.0,<1.25.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• bioconductor-singlecellexperiment >=1.20.0,<1.21.0

• bioconductor-summarizedexperiment >=1.28.0,<1.29.0

• r-base >=4.2,<4.3.0a0

• r-cluster

• r-distr

• r-igraph

• r-pdist

• r-proxy

• r-ruv

Required By:

• bioconductor-singlecelltk

Installation

With an activated Bioconda channel (see 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>)

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