:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-scpipe' .. highlight: bash bioconductor-scpipe =================== .. conda:recipe:: bioconductor-scpipe :replaces_section_title: :noindex: pipeline for single cell RNA\-seq data analysis :homepage: https://bioconductor.org/packages/3.14/bioc/html/scPipe.html :license: GPL (>= 2) :recipe: /`bioconductor-scpipe `_/`meta.yaml `_ A preprocessing pipeline for single cell RNA\-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL\-seq\, MARS\-seq\, Drop\-seq\, Chromium 10x and SMART\-seq protocols. .. conda:package:: bioconductor-scpipe |downloads_bioconductor-scpipe| |docker_bioconductor-scpipe| :versions: .. raw:: html
1.16.0-11.16.0-01.14.0-01.12.0-11.12.0-01.10.0-01.8.0-01.6.0-11.4.1-0 ``1.16.0-1``,  ``1.16.0-0``,  ``1.14.0-0``,  ``1.12.0-1``,  ``1.12.0-0``,  ``1.10.0-0``,  ``1.8.0-0``,  ``1.6.0-1``,  ``1.4.1-0``,  ``1.4.0-0``,  ``1.2.1-0``,  ``1.0.0-0`` .. raw:: html
:depends bioconductor-annotationdbi: ``>=1.56.0,<1.57.0`` :depends bioconductor-biocgenerics: ``>=0.40.0,<0.41.0`` :depends bioconductor-biomart: ``>=2.50.0,<2.51.0`` :depends bioconductor-genomicranges: ``>=1.46.0,<1.47.0`` :depends bioconductor-org.hs.eg.db: ``>=3.14.0,<3.15.0`` :depends bioconductor-org.mm.eg.db: ``>=3.14.0,<3.15.0`` :depends bioconductor-rhtslib: ``>=1.26.0,<1.27.0`` :depends bioconductor-rtracklayer: ``>=1.54.0,<1.55.0`` :depends bioconductor-s4vectors: ``>=0.32.0,<0.33.0`` :depends bioconductor-scater: ``>=1.22.0,<1.23.0`` :depends bioconductor-singlecellexperiment: ``>=1.16.0,<1.17.0`` :depends bioconductor-summarizedexperiment: ``>=1.24.0,<1.25.0`` :depends bioconductor-zlibbioc: ``>=1.40.0,<1.41.0`` :depends libblas: ``>=3.8.0,<4.0a0`` :depends libgcc-ng: ``>=10.3.0`` :depends liblapack: ``>=3.8.0,<4.0a0`` :depends libstdcxx-ng: ``>=10.3.0`` :depends r-base: ``>=4.1,<4.2.0a0`` :depends r-dplyr: :depends r-ggally: :depends r-ggplot2: :depends r-glue: ``>=1.3.0`` :depends r-hash: :depends r-magrittr: :depends r-mass: :depends r-mclust: :depends r-rcpp: ``>=0.11.3`` :depends r-reshape: :depends r-rlang: :depends r-robustbase: :depends r-scales: :depends r-stringr: :depends r-testthat: :requirements: .. rubric:: Installation With an activated Bioconda channel (see :ref:`set-up-channels`), install with:: conda install bioconductor-scpipe and update with:: conda update bioconductor-scpipe or use the docker container:: docker pull quay.io/biocontainers/bioconductor-scpipe: (see `bioconductor-scpipe/tags`_ for valid values for ````) .. |downloads_bioconductor-scpipe| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-scpipe.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-scpipe :alt: (downloads) .. |docker_bioconductor-scpipe| image:: https://quay.io/repository/biocontainers/bioconductor-scpipe/status :target: https://quay.io/repository/biocontainers/bioconductor-scpipe .. _`bioconductor-scpipe/tags`: https://quay.io/repository/biocontainers/bioconductor-scpipe?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-scpipe/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-scpipe/README.html