ScreenR
Package to Perform High Throughput Biological Screening
Bioconductor version: Release (3.20)
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("ScreenR")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | AssayDomain, GeneExpression, Software |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (2 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
| Suggests | rmarkdown (>= 2.11), knitr (>= 1.37), testthat (>= 3.0.0), BiocStyle(>= 2.22.0), covr (>= 3.5) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | ScreenR_1.8.0.tar.gz |
| Windows Binary (x86_64) | ScreenR_1.8.0.zip (64-bit only) |
| macOS Binary (x86_64) | ScreenR_1.8.0.tgz |
| macOS Binary (arm64) | ScreenR_1.8.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ScreenR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ScreenR |
| Bioc Package Browser | https://code.bioconductor.org/browse/ScreenR/ |
| Package Short Url | https://bioconductor.org/packages/ScreenR/ |
| Package Downloads Report | Download Stats |