recipe bioconductor-batchelor

Single-Cell Batch Correction Methods

Homepage:

https://bioconductor.org/packages/3.18/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

(downloads) docker_bioconductor-batchelor

versions:
1.18.0-01.16.0-01.14.0-11.14.0-01.10.0-21.10.0-11.10.0-01.8.0-01.6.2-0

1.18.0-01.16.0-01.14.0-11.14.0-01.10.0-21.10.0-11.10.0-01.8.0-01.6.2-01.6.0-01.4.0-01.2.1-01.0.1-0

depends bioconductor-beachmat:

>=2.18.0,<2.19.0

depends bioconductor-beachmat:

>=2.18.0,<2.19.0a0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-biocgenerics:

>=0.48.1,<0.49.0a0

depends bioconductor-biocneighbors:

>=1.20.0,<1.21.0

depends bioconductor-biocneighbors:

>=1.20.0,<1.21.0a0

depends bioconductor-biocparallel:

>=1.36.0,<1.37.0

depends bioconductor-biocparallel:

>=1.36.0,<1.37.0a0

depends bioconductor-biocsingular:

>=1.18.0,<1.19.0

depends bioconductor-biocsingular:

>=1.18.0,<1.19.0a0

depends bioconductor-delayedarray:

>=0.28.0,<0.29.0

depends bioconductor-delayedarray:

>=0.28.0,<0.29.0a0

depends bioconductor-delayedmatrixstats:

>=1.24.0,<1.25.0

depends bioconductor-delayedmatrixstats:

>=1.24.0,<1.25.0a0

depends bioconductor-residualmatrix:

>=1.12.0,<1.13.0

depends bioconductor-residualmatrix:

>=1.12.0,<1.13.0a0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-s4vectors:

>=0.40.2,<0.41.0a0

depends bioconductor-scaledmatrix:

>=1.10.0,<1.11.0

depends bioconductor-scaledmatrix:

>=1.10.0,<1.11.0a0

depends bioconductor-scuttle:

>=1.12.0,<1.13.0

depends bioconductor-scuttle:

>=1.12.0,<1.13.0a0

depends bioconductor-singlecellexperiment:

>=1.24.0,<1.25.0

depends bioconductor-singlecellexperiment:

>=1.24.0,<1.25.0a0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx-ng:

>=12

depends r-base:

>=4.3,<4.4.0a0

depends r-igraph:

depends r-matrix:

depends r-rcpp:

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-batchelor

and update with::

   mamba update bioconductor-batchelor

To create a new environment, run:

mamba create --name myenvname bioconductor-batchelor

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, 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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