: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 multi\-omic data pre\-processing :homepage: https://bioconductor.org/packages/3.20/bioc/html/scPipe.html :license: GPL (>= 2) :recipe: /`bioconductor-scpipe `_/`meta.yaml `_ A preprocessing pipeline for single cell RNA\-seq\/ATAC\-seq data that starts from the fastq files and produces a feature 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
2.6.0-02.2.0-02.0.0-01.19.0-11.19.0-01.16.1-01.16.0-11.16.0-01.14.0-0 ``2.6.0-0``,  ``2.2.0-0``,  ``2.0.0-0``,  ``1.19.0-1``,  ``1.19.0-0``,  ``1.16.1-0``,  ``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: ``>=1.68.0,<1.69.0`` :depends bioconductor-annotationdbi: ``>=1.68.0,<1.69.0a0`` :depends bioconductor-basilisk: ``>=1.18.0,<1.19.0`` :depends bioconductor-basilisk: ``>=1.18.0,<1.19.0a0`` :depends bioconductor-biocgenerics: ``>=0.52.0,<0.53.0`` :depends bioconductor-biocgenerics: ``>=0.52.0,<0.53.0a0`` :depends bioconductor-biomart: ``>=2.62.0,<2.63.0`` :depends bioconductor-biomart: ``>=2.62.0,<2.63.0a0`` :depends bioconductor-biostrings: ``>=2.74.0,<2.75.0`` :depends bioconductor-biostrings: ``>=2.74.0,<2.75.0a0`` :depends bioconductor-dropletutils: ``>=1.26.0,<1.27.0`` :depends bioconductor-dropletutils: ``>=1.26.0,<1.27.0a0`` :depends bioconductor-genomicalignments: ``>=1.42.0,<1.43.0`` :depends bioconductor-genomicalignments: ``>=1.42.0,<1.43.0a0`` :depends bioconductor-genomicranges: ``>=1.58.0,<1.59.0`` :depends bioconductor-genomicranges: ``>=1.58.0,<1.59.0a0`` :depends bioconductor-iranges: ``>=2.40.0,<2.41.0`` :depends bioconductor-iranges: ``>=2.40.0,<2.41.0a0`` :depends bioconductor-multiassayexperiment: ``>=1.32.0,<1.33.0`` :depends bioconductor-multiassayexperiment: ``>=1.32.0,<1.33.0a0`` :depends bioconductor-org.hs.eg.db: ``>=3.20.0,<3.21.0`` :depends bioconductor-org.hs.eg.db: ``>=3.20.0,<3.21.0a0`` :depends bioconductor-org.mm.eg.db: ``>=3.20.0,<3.21.0`` :depends bioconductor-org.mm.eg.db: ``>=3.20.0,<3.21.0a0`` :depends bioconductor-rhtslib: ``>=3.2.0,<3.3.0`` :depends bioconductor-rhtslib: ``>=3.2.0,<3.3.0a0`` :depends bioconductor-rsamtools: ``>=2.22.0,<2.23.0`` :depends bioconductor-rsamtools: ``>=2.22.0,<2.23.0a0`` :depends bioconductor-rsubread: ``>=2.20.0,<2.21.0`` :depends bioconductor-rsubread: ``>=2.20.0,<2.21.0a0`` :depends bioconductor-rtracklayer: ``>=1.66.0,<1.67.0`` :depends bioconductor-rtracklayer: ``>=1.66.0,<1.67.0a0`` :depends bioconductor-s4vectors: ``>=0.44.0,<0.45.0`` :depends bioconductor-s4vectors: ``>=0.44.0,<0.45.0a0`` :depends bioconductor-singlecellexperiment: ``>=1.28.0,<1.29.0`` :depends bioconductor-singlecellexperiment: ``>=1.28.0,<1.29.0a0`` :depends bioconductor-summarizedexperiment: ``>=1.36.0,<1.37.0`` :depends bioconductor-summarizedexperiment: ``>=1.36.0,<1.37.0a0`` :depends bioconductor-zlibbioc: ``>=1.52.0,<1.53.0`` :depends bioconductor-zlibbioc: ``>=1.52.0,<1.53.0a0`` :depends libblas: ``>=3.9.0,<4.0a0`` :depends libgcc: ``>=13`` :depends liblapack: ``>=3.9.0,<4.0a0`` :depends liblzma: ``>=5.6.3,<6.0a0`` :depends libstdcxx: ``>=13`` :depends libzlib: ``>=1.3.1,<2.0a0`` :depends r-base: ``>=4.4,<4.5.0a0`` :depends r-data.table: :depends r-dplyr: :depends r-flexmix: :depends r-ggally: :depends r-ggplot2: :depends r-glue: ``>=1.3.0`` :depends r-hash: :depends r-magrittr: :depends r-mass: :depends r-matrix: ``>=1.5.0`` :depends r-mclust: :depends r-purrr: :depends r-rcpp: ``>=0.11.3`` :depends r-reshape: :depends r-reticulate: :depends r-rlang: :depends r-robustbase: :depends r-scales: :depends r-stringr: :depends r-testthat: :depends r-tibble: :depends r-tidyr: :depends r-vctrs: ``>=0.5.2`` :requirements: :additional platforms: .. 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-scpipe and update with:: mamba update bioconductor-scpipe To create a new environment, run:: mamba create --name myenvname bioconductor-scpipe 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-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