recipe bioconductor-screenr

Package to Perform High Throughput Biological Screening

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/ScreenR.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-screenr/meta.yaml

ScreenR is a package suitable to perform hit identification in loss of function High Throughput Biological Screenings performed using barcoded shRNA-based libraries. ScreenR combines the computing power of software such as edgeR with the simplicity of use of the Tidyverse metapackage. ScreenR executes a pipeline able to find candidate hits from barcode counts, and integrates a wide range of visualization modes for each step of the analysis.

package bioconductor-screenr

versions:

1.8.0-0,  1.4.0-0,  1.2.0-0,  1.0.0-0

depends bioconductor-edger:

>=4.4.0,<4.5.0

depends bioconductor-limma:

>=3.62.0,<3.63.0

depends r-base:

>=4.4,<4.5.0a0

depends r-dplyr:

>=1.0

depends r-ggplot2:

>=3.3

depends r-ggvenn:

>=0.1.9

depends r-magrittr:

>=1.0

depends r-patchwork:

>=1.1

depends r-purrr:

>=0.3.4

depends r-rlang:

>=0.4

depends r-scales:

>=1.1.1

depends r-stringr:

>=1.4

depends r-tibble:

>=3.1.6

depends r-tidyr:

>=1.2

depends r-tidyselect:

>=1.1.2

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-screenr

and update with::

   mamba update bioconductor-screenr

To create a new environment, run:

mamba create --name myenvname bioconductor-screenr

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-screenr:<tag>

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

Download stats

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-screenr/README.html)