- recipe bioconductor-batchelor
Single-Cell Batch Correction Methods
- Homepage:
https://bioconductor.org/packages/3.18/bioc/html/batchelor.html
- License:
GPL-3.0-only
- Recipe:
- Links:
biotools: batchelor
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:
1.18.0-1,1.18.0-0,1.16.0-0,1.14.0-1,1.14.0-0,1.10.0-2,1.10.0-1,1.10.0-0,1.8.0-0,1.18.0-1,1.18.0-0,1.16.0-0,1.14.0-1,1.14.0-0,1.10.0-2,1.10.0-1,1.10.0-0,1.8.0-0,1.6.2-0,1.6.0-0,1.4.0-0,1.2.1-0,1.0.1-0- depends bioconductor-beachmat:
>=2.18.0,<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
myenvnamebeing 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>``)
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-batchelor/README.html)
