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screenCounter

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

Counting Reads in High-Throughput Sequencing Screens

Bioconductor version: Development (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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.1.3
In Bioconductor since BioC 3.17 (R-4.3) (< 6 months)
License MIT + file LICENSE
Depends S4Vectors, SummarizedExperiment
Imports Rcpp, zlibbioc, BiocParallel
Linking To Rcpp
Suggests Biostrings, BiocStyle, knitr, rmarkdown, testthat
System Requirements C++17, GNU make
Enhances
URL https://github.com/crisprVerse/screenCounter
Bug Reports https://github.com/crisprVerse/screenCounter/issues
See More
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_1.1.3.tar.gz
Windows Binary screenCounter_1.1.3.zip (64-bit only)
macOS Binary (x86_64) screenCounter_1.1.3.tgz
macOS Binary (arm64) screenCounter_1.1.3.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