:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-cellarepertorium' .. highlight: bash bioconductor-cellarepertorium ============================= .. conda:recipe:: bioconductor-cellarepertorium :replaces_section_title: :noindex: Data structures\, clustering and testing for single cell immune receptor repertoires \(scRNAseq RepSeq\/AIRR\-seq\) :homepage: https://bioconductor.org/packages/3.18/bioc/html/CellaRepertorium.html :license: GPL-3 :recipe: /`bioconductor-cellarepertorium `_/`meta.yaml `_ Methods to cluster and analyze high\-throughput single cell immune cell repertoires\, especially from the 10X Genomics VDJ solution. Contains an R interface to CD\-HIT \(Li and Godzik 2006\). Methods to visualize and analyze paired heavy\-light chain data. Tests for specific expansion\, as well as omnibus oligoclonality under hypergeometric models. .. conda:package:: bioconductor-cellarepertorium |downloads_bioconductor-cellarepertorium| |docker_bioconductor-cellarepertorium| :versions: .. raw:: html
1.12.0-01.10.0-01.8.0-11.8.0-01.4.0-21.4.0-11.4.0-01.2.0-01.0.0-2 ``1.12.0-0``,  ``1.10.0-0``,  ``1.8.0-1``,  ``1.8.0-0``,  ``1.4.0-2``,  ``1.4.0-1``,  ``1.4.0-0``,  ``1.2.0-0``,  ``1.0.0-2``,  ``1.0.0-1`` .. raw:: html
:depends bioconductor-biocgenerics: ``>=0.48.0,<0.49.0`` :depends bioconductor-biocgenerics: ``>=0.48.1,<0.49.0a0`` :depends bioconductor-biostrings: ``>=2.70.0,<2.71.0`` :depends bioconductor-biostrings: ``>=2.70.1,<2.71.0a0`` :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0`` :depends bioconductor-s4vectors: ``>=0.40.2,<0.41.0a0`` :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-dplyr: :depends r-forcats: :depends r-generics: :depends r-glue: :depends r-matrix: :depends r-progress: :depends r-purrr: :depends r-rcpp: :depends r-reshape2: :depends r-rlang: ``>=0.3`` :depends r-stringr: :depends r-tibble: :depends r-tidyr: :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-cellarepertorium and update with:: mamba update bioconductor-cellarepertorium To create a new environment, run:: mamba create --name myenvname bioconductor-cellarepertorium 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-cellarepertorium: (see `bioconductor-cellarepertorium/tags`_ for valid values for ````) .. |downloads_bioconductor-cellarepertorium| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-cellarepertorium.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-cellarepertorium :alt: (downloads) .. |docker_bioconductor-cellarepertorium| image:: https://quay.io/repository/biocontainers/bioconductor-cellarepertorium/status :target: https://quay.io/repository/biocontainers/bioconductor-cellarepertorium .. _`bioconductor-cellarepertorium/tags`: https://quay.io/repository/biocontainers/bioconductor-cellarepertorium?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-cellarepertorium/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-cellarepertorium/README.html