Package Recipe 'bioconductor-screenr'

recipe bioconductor-screenr

Package to Perform High Throughput Biological Screening

Homepage:: https://bioconductor.org/packages/3.20/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:

1.12.1-0, 1.8.0-0, 1.4.0-0, 1.2.0-0, 1.0.0-0

Depends:

on bioconductor-edger >=4.8.0,<4.9.0
on bioconductor-limma >=3.66.0,<3.67.0
on r-base >=4.5,<4.6.0a0
on r-dplyr >=1.0
on r-ggplot2 >=3.3
on r-ggvenn >=0.1.9
on r-magrittr >=1.0
on r-patchwork >=1.1
on r-purrr >=0.3.4
on r-rlang >=0.4
on r-scales >=1.1.1
on r-stringr >=1.4
on r-tibble >=3.1.6
on r-tidyr >=1.2
on r-tidyselect >=1.1.2

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-screenr

to add into an existing workspace instead, run:

pixi add bioconductor-screenr

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-screenr

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-screenr

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

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

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

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)