ScreenR
This is the released version of ScreenR; for the devel version, see ScreenR.
Package to Perform High Throughput Biological Screening
Bioconductor version: Release (3.23)
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("ScreenR")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.14.0 |
| 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 |
See More
| 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 | |
| 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_1.14.0.tar.gz |
| Windows Binary (x86_64) | ScreenR_1.13.1.zip |
| macOS Binary (big-sur-x86_64) | ScreenR_1.14.0.tgz |
| macOS Binary (sonoma-arm64) | ScreenR_1.14.0.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 |