ScreenR

DOI: 10.18129/B9.bioc.ScreenR    

This is the development version of ScreenR; to use it, please install the devel version of Bioconductor.

Package to Perform High Throughput Biological Screening

Bioconductor version: Development (3.16)

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] (0000-0002-2301-6465), Elena Ceccacci [aut] (0000-0002-2285-8994), Saverio Minucci [fnd, ths] (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 "4.2") 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")

 

HTML R Script ScreenR Example Analysis
PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews AssayDomain, GeneExpression, Software
Version 0.99.53
In Bioconductor since BioC 3.16 (R-4.2)
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)
LinkingTo
Suggests rmarkdown (>= 2.11), knitr (>= 1.37), testthat (>= 3.0.0), BiocStyle(>= 2.22.0), covr (>= 3.5)
SystemRequirements
Enhances
URL https://emanuelsoda.github.io/ScreenR/
BugReports https://github.com/EmanuelSoda/ScreenR/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package ScreenR_0.99.53.tar.gz
Windows Binary ScreenR_0.99.53.zip (64-bit only)
macOS 10.13 (High Sierra) ScreenR_0.99.53.tgz
Source Repository git clone https://git.bioconductor.org/packages/ScreenR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ScreenR
Package Short Url https://bioconductor.org/packages/ScreenR/
Package Downloads Report Download Stats

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