screenCounter
Counting Reads in High-Throughput Sequencing Screens
Bioconductor version: Release (3.20)
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 "4.4") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Alignment, CRISPR, FunctionalGenomics, FunctionalPrediction, Software |
| Version | 1.6.0 |
| In Bioconductor since | BioC 3.17 (R-4.3) (1.5 years) |
| 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_1.6.0.tar.gz |
| Windows Binary (x86_64) | screenCounter_1.6.0.zip |
| macOS Binary (x86_64) | screenCounter_1.6.0.tgz |
| macOS Binary (arm64) | screenCounter_1.5.1.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 |