:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-batchelor' .. highlight: bash bioconductor-batchelor ====================== .. conda:recipe:: bioconductor-batchelor :replaces_section_title: :noindex: 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. .. conda:package:: bioconductor-batchelor |downloads_bioconductor-batchelor| |docker_bioconductor-batchelor| :versions: .. raw:: html
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 ``1.18.0-0``,  ``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`` .. raw:: html
: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: .. rubric:: Installation You need a conda-compatible package manager (currently either `micromamba `_, `mamba `_, or `conda `_) and the Bioconda channel already activated (see :ref:`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: (see `bioconductor-batchelor/tags`_ for valid values for ````) .. |downloads_bioconductor-batchelor| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-batchelor.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-batchelor :alt: (downloads) .. |docker_bioconductor-batchelor| image:: https://quay.io/repository/biocontainers/bioconductor-batchelor/status :target: https://quay.io/repository/biocontainers/bioconductor-batchelor .. _`bioconductor-batchelor/tags`: https://quay.io/repository/biocontainers/bioconductor-batchelor?tab=tags .. raw:: html Download stats ----------------- .. raw:: html :file: ../../templates/package_dashboard.html Link to this page ----------------- Render an |install-with-bioconda| 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) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/bioconductor-batchelor/README.html