recipe bioconductor-batchelor

Single-Cell Batch Correction Methods

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/batchelor.html

License:

GPL-3

Recipe:

/bioconductor-batchelor/meta.yaml

Implements a variety of methods for batch correction of single-cell (RNA sequencing) data. This includes methods based on detecting mutually nearest neighbors, as well as several efficient variants of linear regression of the log-expression values. Functions are also provided to perform global rescaling to remove differences in depth between batches, and to perform a principal components analysis that is robust to differences in the numbers of cells across batches.

package bioconductor-batchelor

Versions:

1.14.0-0,  1.10.0-2,  1.10.0-1,  1.10.0-0,  1.8.0-0,  1.6.2-0,  1.6.0-0,  1.4.0-0,  1.2.1-0, 

1.14.0-0,  1.10.0-2,  1.10.0-1,  1.10.0-0,  1.8.0-0,  1.6.2-0,  1.6.0-0,  1.4.0-0,  1.2.1-0,  1.0.1-0

Depends:

• bioconductor-beachmat >=2.14.0,<2.15.0

• bioconductor-biocgenerics >=0.44.0,<0.45.0

• bioconductor-biocneighbors >=1.16.0,<1.17.0

• 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-residualmatrix >=1.8.0,<1.9.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• bioconductor-scaledmatrix >=1.6.0,<1.7.0

• bioconductor-scuttle >=1.8.0,<1.9.0

• bioconductor-singlecellexperiment >=1.20.0,<1.21.0

• bioconductor-summarizedexperiment >=1.28.0,<1.29.0

• libblas >=3.9.0,<4.0a0

• libgcc-ng >=12

• liblapack >=3.9.0,<4.0a0

• libstdcxx-ng >=12

• r-base >=4.2,<4.3.0a0

• r-igraph

• r-matrix

• r-rcpp

Required By:

• r-monocle3

• bioconductor-chromscape

• bioconductor-mumosa

• bioconductor-singlecelltk

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-batchelor

and update with:

conda update bioconductor-batchelor

or use the docker container:

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

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

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