:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-synlet' .. highlight: bash bioconductor-synlet =================== .. conda:recipe:: bioconductor-synlet :replaces_section_title: :noindex: Hits Selection for Synthetic Lethal RNAi Screen Data :homepage: https://bioconductor.org/packages/3.18/bioc/html/synlet.html :license: GPL-3 :recipe: /`bioconductor-synlet `_/`meta.yaml `_ :links: biotools: :biotools:`synlet`, doi: :doi:`10.1101/043570` Select hits from synthetic lethal RNAi screen data. For example\, there are two identical celllines except one gene is knocked\-down in one cellline. The interest is to find genes that lead to stronger lethal effect when they are knocked\-down further by siRNA. Quality control and various visualisation tools are implemented. Four different algorithms could be used to pick up the interesting hits. This package is designed based on 384 wells plates\, but may apply to other platforms with proper configuration. .. conda:package:: bioconductor-synlet |downloads_bioconductor-synlet| |docker_bioconductor-synlet| :versions: .. raw:: html
2.2.0-02.0.0-01.28.0-01.24.0-01.22.0-01.20.0-11.20.0-01.18.0-01.16.0-0 ``2.2.0-0``,  ``2.0.0-0``,  ``1.28.0-0``,  ``1.24.0-0``,  ``1.22.0-0``,  ``1.20.0-1``,  ``1.20.0-0``,  ``1.18.0-0``,  ``1.16.0-0``,  ``1.14.0-1``,  ``1.14.0-0``,  ``1.12.1-0``,  ``1.12.0-0``,  ``1.10.0-0``,  ``1.8.0-0`` .. raw:: html
:depends bioconductor-rankprod: ``>=3.28.0,<3.29.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-data.table: :depends r-ggplot2: :depends r-magrittr: :depends r-patchwork: :depends r-rcolorbrewer: :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-synlet and update with:: mamba update bioconductor-synlet To create a new environment, run:: mamba create --name myenvname bioconductor-synlet 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-synlet: (see `bioconductor-synlet/tags`_ for valid values for ````) .. |downloads_bioconductor-synlet| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-synlet.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-synlet :alt: (downloads) .. |docker_bioconductor-synlet| image:: https://quay.io/repository/biocontainers/bioconductor-synlet/status :target: https://quay.io/repository/biocontainers/bioconductor-synlet .. _`bioconductor-synlet/tags`: https://quay.io/repository/biocontainers/bioconductor-synlet?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-synlet/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-synlet/README.html