recipe bioconductor-synlet

Hits Selection for Synthetic Lethal RNAi Screen Data

Homepage

https://bioconductor.org/packages/3.11/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

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 >=3.14.0,<3.15.0

• r-base >=4.0,<4.1.0a0

• r-doby

• r-dplyr

• r-ggplot2

• r-magrittr

• r-rcolorbrewer

• r-reshape2

Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-synlet

and update with:

conda update bioconductor-synlet

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-synlet:<tag>

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

Link to this page

Render an 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)