:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-sccb2' .. highlight: bash bioconductor-sccb2 ================== .. conda:recipe:: bioconductor-sccb2 :replaces_section_title: :noindex: CB2 improves power of cell detection in droplet\-based single\-cell RNA sequencing data :homepage: https://bioconductor.org/packages/3.18/bioc/html/scCB2.html :license: GPL-3 :recipe: /`bioconductor-sccb2 `_/`meta.yaml `_ scCB2 is an R package implementing CB2 for distinguishing real cells from empty droplets in droplet\-based single cell RNA\-seq experiments \(especially for 10x Chromium\). It is based on clustering similar barcodes and calculating Monte\-Carlo p\-value for each cluster to test against background distribution. This cluster\-level test outperforms single\-barcode\-level tests in dealing with low count barcodes and homogeneous sequencing library\, while keeping FDR well controlled. .. conda:package:: bioconductor-sccb2 |downloads_bioconductor-sccb2| |docker_bioconductor-sccb2| :versions: ``1.12.0-0``,  ``1.10.0-0``,  ``1.8.0-0``,  ``1.4.0-0``,  ``1.2.0-0``,  ``1.0.0-1``,  ``1.0.0-0`` :depends bioconductor-dropletutils: ``>=1.22.0,<1.23.0`` :depends bioconductor-edger: ``>=4.0.0,<4.1.0`` :depends bioconductor-rhdf5: ``>=2.46.0,<2.47.0`` :depends bioconductor-singlecellexperiment: ``>=1.24.0,<1.25.0`` :depends bioconductor-summarizedexperiment: ``>=1.32.0,<1.33.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-doparallel: :depends r-foreach: :depends r-iterators: :depends r-matrix: :depends r-seurat: :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-sccb2 and update with:: mamba update bioconductor-sccb2 To create a new environment, run:: mamba create --name myenvname bioconductor-sccb2 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-sccb2: (see `bioconductor-sccb2/tags`_ for valid values for ````) .. |downloads_bioconductor-sccb2| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-sccb2.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-sccb2 :alt: (downloads) .. |docker_bioconductor-sccb2| image:: https://quay.io/repository/biocontainers/bioconductor-sccb2/status :target: https://quay.io/repository/biocontainers/bioconductor-sccb2 .. _`bioconductor-sccb2/tags`: https://quay.io/repository/biocontainers/bioconductor-sccb2?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-sccb2/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-sccb2/README.html