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Bioconductor - ScreenR (development version)

ScreenR

This is the development version of ScreenR; for the stable release version, see ScreenR.

Package to Perform High Throughput Biological Screening

Bioconductor version: Development (3.22)

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.

Author: Emanuel Michele Soda [aut, cre] (ORICD: 0000-0002-2301-6465), Elena Ceccacci [aut] (ORICD: 0000-0002-2285-8994), Saverio Minucci [fnd, ths] (ORICD: 0000-0001-5678-536X)

Maintainer: Emanuel Michele Soda <emanuelsoda at gmail.com>

Citation (from within R, enter citation("ScreenR")): Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("ScreenR")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("ScreenR")
Details biocViews AssayDomain, GeneExpression, Software Version 1.11.0 In Bioconductor since BioC 3.16 (R-4.2) (2.5 years) License MIT + file LICENSE Depends R (>= 4.2) Imports methods (>= 4.0), rlang (>= 0.4), stringr (>= 1.4), limma(>= 3.46), patchwork (>= 1.1), tibble (>= 3.1.6), scales (>= 1.1.1), ggvenn (>= 0.1.9), purrr (>= 0.3.4), ggplot2 (>= 3.3), stats, tidyr (>= 1.2), magrittr (>= 1.0), dplyr (>= 1.0), edgeR(>= 3.32), tidyselect (>= 1.1.2) System Requirements URL https://emanuelsoda.github.io/ScreenR/ Bug Reports https://github.com/EmanuelSoda/ScreenR/issues See More Package Archives

Follow Installation instructions to use this package in your R session.

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