:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-seqsqc' .. highlight: bash bioconductor-seqsqc =================== .. conda:recipe:: bioconductor-seqsqc :replaces_section_title: :noindex: A bioconductor package for sample quality check with next generation sequencing data :homepage: https://bioconductor.org/packages/3.18/bioc/html/SeqSQC.html :license: GPL-3 :recipe: /`bioconductor-seqsqc `_/`meta.yaml `_ The SeqSQC is designed to identify problematic samples in NGS data\, including samples with gender mismatch\, contamination\, cryptic relatedness\, and population outlier. .. conda:package:: bioconductor-seqsqc |downloads_bioconductor-seqsqc| |docker_bioconductor-seqsqc| :versions: .. raw:: html
1.24.0-01.22.0-01.20.0-01.16.0-01.14.0-01.12.0-11.12.0-01.10.0-01.8.0-0 ``1.24.0-0``,  ``1.22.0-0``,  ``1.20.0-0``,  ``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``,  ``1.4.0-0`` .. raw:: html
:depends bioconductor-experimenthub: ``>=2.10.0,<2.11.0`` :depends bioconductor-gdsfmt: ``>=1.38.0,<1.39.0`` :depends bioconductor-genomicranges: ``>=1.54.0,<1.55.0`` :depends bioconductor-iranges: ``>=2.36.0,<2.37.0`` :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0`` :depends bioconductor-snprelate: ``>=1.36.0,<1.37.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-e1071: :depends r-ggally: :depends r-ggplot2: :depends r-rbokeh: :depends r-rcolorbrewer: :depends r-reshape2: :depends r-rmarkdown: :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-seqsqc and update with:: mamba update bioconductor-seqsqc To create a new environment, run:: mamba create --name myenvname bioconductor-seqsqc 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-seqsqc: (see `bioconductor-seqsqc/tags`_ for valid values for ````) .. |downloads_bioconductor-seqsqc| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-seqsqc.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-seqsqc :alt: (downloads) .. |docker_bioconductor-seqsqc| image:: https://quay.io/repository/biocontainers/bioconductor-seqsqc/status :target: https://quay.io/repository/biocontainers/bioconductor-seqsqc .. _`bioconductor-seqsqc/tags`: https://quay.io/repository/biocontainers/bioconductor-seqsqc?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-seqsqc/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-seqsqc/README.html