Bioconductor - CellBarcode

This is the released version of CellBarcode; for the devel version, see CellBarcode.

Cellular DNA Barcode Analysis toolkit

Bioconductor version: Release (3.22)

The package CellBarcode performs Cellular DNA Barcode analysis. It can handle all kinds of DNA barcodes, as long as the barcode is within a single sequencing read and has a pattern that can be matched by a regular expression. \code{CellBarcode} can handle barcodes with flexible lengths, with or without UMI (unique molecular identifier). This tool also can be used for pre-processing some amplicon data such as CRISPR gRNA screening, immune repertoire sequencing, and metagenome data.

Author: Wenjie Sun [cre, aut] ORCID: 0000-0002-3100-2346 , Anne-Marie Lyne [aut], Leila Perie [aut]

Maintainer: Wenjie Sun <sunwjie at gmail.com>

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

Installation

To install this package, start R (version "4.5") and enter:


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

BiocManager::install("CellBarcode")

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("CellBarcode")

Details

biocViews	CRISPR, Preprocessing, QualityControl, Sequencing, Software
Version	1.16.0
In Bioconductor since	BioC 3.14 (R-4.1) (4.5 years)
License	Artistic-2.0
Depends	R (>= 4.1.0)
Imports	methods, stats, Rcpp (>= 1.0.5), data.table (>= 1.12.6), plyr, ggplot2, stringr, magrittr, ShortRead(>= 1.48.0), Biostrings(>= 2.58.0), egg, Ckmeans.1d.dp, utils, S4Vectors, seqinr, Rsamtools
System Requirements
URL	https://wenjie1991.github.io/CellBarcode/
Bug Reports	https://github.com/wenjie1991/CellBarcode/issues

Package Archives

Follow Installation instructions to use this package in your R session.