recipe bioconductor-batchelor

Single-Cell Batch Correction Methods

Homepage

https://bioconductor.org/packages/3.12/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

1.6.0-0,  1.4.0-0,  1.2.1-0,  1.0.1-0

Depends

• bioconductor-biocgenerics >=0.36.0,<0.37.0

• bioconductor-biocneighbors >=1.8.0,<1.9.0

• bioconductor-biocparallel >=1.24.0,<1.25.0

• bioconductor-biocsingular >=1.6.0,<1.7.0

• bioconductor-delayedarray >=0.16.0,<0.17.0

• bioconductor-delayedmatrixstats >=1.12.0,<1.13.0

• bioconductor-residualmatrix >=1.0.0,<1.1.0

• bioconductor-s4vectors >=0.28.0,<0.29.0

• bioconductor-scuttle >=1.0.0,<1.1.0

• bioconductor-singlecellexperiment >=1.12.0,<1.13.0

• bioconductor-summarizedexperiment >=1.20.0,<1.21.0

• libblas >=3.8.0,<4.0a0

• libgcc-ng >=7.5.0

• liblapack >=3.8.0,<4.0a0

• libstdcxx-ng >=7.5.0

• r-base >=4.0,<4.1.0a0

• r-igraph

• r-matrix

• r-rcpp

Required By

• bioconductor-singlecelltk

• r-monocle3

• bioconductor-chromscape

Installation

With an activated Bioconda channel (see 2. 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>)

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-batchelor/README.html)