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screenCounter

Counting Reads in High-Throughput Sequencing Screens


Bioconductor version: Release (3.18)

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>

Citation (from within R, enter citation("screenCounter")):

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

Details

biocViews Alignment, CRISPR, FunctionalGenomics, FunctionalPrediction, Software
Version 1.2.0
In Bioconductor since BioC 3.17 (R-4.3) (1 year)
License MIT + file LICENSE
Depends S4Vectors, SummarizedExperiment
Imports Rcpp, zlibbioc, BiocParallel
System Requirements C++17, GNU make
URL https://github.com/crisprVerse/screenCounter
Bug Reports https://github.com/crisprVerse/screenCounter/issues
See More
Suggests BiocGenerics, Biostrings, BiocStyle, knitr, rmarkdown, testthat
Linking To Rcpp
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 screenCounter_1.2.0.tar.gz
Windows Binary screenCounter_1.2.0.zip
macOS Binary (x86_64) screenCounter_1.2.0.tgz
macOS Binary (arm64) screenCounter_1.2.0.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