recipe bioconductor-synlet

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: synlet, 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.

package bioconductor-synlet

versions:

2.6.0-0,  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, 

2.6.0-0,  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

depends bioconductor-rankprod:

>=3.32.0,<3.33.0

depends r-base:

>=4.4,<4.5.0a0

depends r-data.table:

depends r-ggplot2:

depends r-magrittr:

depends r-patchwork:

depends r-rcolorbrewer:

requirements:

additional platforms:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see 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:<tag>

(see `bioconductor-synlet/tags`_ for valid values for ``<tag>``)

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