screenCounter

DOI: 10.18129/B9.bioc.screenCounter  

Counting Reads in High-Throughput Sequencing Screens

Bioconductor version: Release (3.17)

Provides functions for counting reads from high-throughput sequencing screen data (e.g., CRISPR, shRNA) to quantify barcode abundance. Currently supports single barcodes in single- or paired-end data, and combinatorial barcodes in paired-end data.

Author: Aaron Lun [aut, cre]

Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>

Installation

To install this package, start R (version "4.3") and enter:

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

BiocManager::install("screenCounter")

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("screenCounter")

 

HTML	R Script	Counting barcodes
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Alignment, CRISPR, FunctionalGenomics, FunctionalPrediction, Software
Version	1.0.1
In Bioconductor since	BioC 3.17 (R-4.3) (< 6 months)
License	MIT + file LICENSE
Depends	S4Vectors, SummarizedExperiment
Imports	Rcpp, zlibbioc, BiocParallel
LinkingTo	Rcpp
Suggests	Biostrings, BiocStyle, knitr, rmarkdown, testthat
SystemRequirements	C++17
Enhances
URL	https://github.com/crisprVerse/screenCounter
BugReports	https://github.com/crisprVerse/screenCounter/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	screenCounter_1.0.1.tar.gz
Windows Binary	screenCounter_1.0.1.zip (64-bit only)
macOS Binary (x86_64)	screenCounter_1.0.1.tgz
macOS Binary (arm64)	screenCounter_1.0.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/screenCounter
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/screenCounter
Bioc Package Browser	https://code.bioconductor.org/browse/screenCounter/
Package Short Url	https://bioconductor.org/packages/screenCounter/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive