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CellBarcode

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

Cellular DNA Barcode Analysis toolkit


Bioconductor version: Development (3.21)

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: ), 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")

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

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")
10X_Barcode HTML R Script
UMI_Barcode HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews CRISPR, Preprocessing, QualityControl, Sequencing, Software
Version 1.13.2
In Bioconductor since BioC 3.14 (R-4.1) (3.5 years)
License Artistic-2.0
Depends R (>= 4.1.0)
Imports methods, stats, 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 Cargo (Rust's package manager), rustc
URL https://wenjie1991.github.io/CellBarcode/
Bug Reports https://github.com/wenjie1991/CellBarcode/issues
See More
Suggests BiocStyle, testthat (>= 3.0.0), knitr, rmarkdown
Linking To BH
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 CellBarcode_1.13.2.tar.gz
Windows Binary (x86_64) CellBarcode_1.13.1.zip (64-bit only)
macOS Binary (x86_64) CellBarcode_1.13.1.tgz
macOS Binary (arm64) CellBarcode_1.13.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/CellBarcode
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CellBarcode
Bioc Package Browser https://code.bioconductor.org/browse/CellBarcode/
Package Short Url https://bioconductor.org/packages/CellBarcode/
Package Downloads Report Download Stats