ScreenR

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16

Package to Perform High Throughput Biological Screening

Bioconductor version: Development (3.24)

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")):

Emanuel Michele Soda, Elena Ceccacci. ScreenR: Package to Perform High Throughput Biological Screening. doi:10.18129/B9.bioc.ScreenR, R package version 1.15.0, https://bioconductor.org/packages/ScreenR.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	AssayDomain, GeneExpression, Software
Version	1.15.0
In Bioconductor since	BioC 3.16 (R-4.2) (4 years)
License	MIT + file LICENSE
Depends	R (>= 4.3)
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

Suggests	rmarkdown (>= 2.11), markdown, knitr (>= 1.37), testthat (>= 3.0.0), BiocStyle (>= 2.22.0), covr (>= 3.5)
Linking To
Enhances
Depends On Me
Imports Me
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Build Report	Build Report, r-universe

Package Archives

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

Source Package	ScreenR_1.15.0.tar.gz
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)	ScreenR_1.15.0.tgz
macOS Binary (sonoma-arm64)	ScreenR_1.15.0.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