CellBarcode
This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see CellBarcode.
Cellular DNA Barcode Analysis toolkit
Bioconductor version: 3.16
This package performs Cellular DNA Barcode (genetic lineage tracing) analysis. The package can handle all kinds of DNA barcodes, as long as the barcode within a single sequencing read and has a pattern which can be matched by a regular expression. This package can handle barcode with flexible length, with or without UMI (unique molecular identifier). This tool also can be used for pre-processing of some amplicon sequencing such as CRISPR gRNA screening, immune repertoire sequencing and meta genome data.
Author: Wenjie Sun [cre], Anne-Marie Lyne [aut], Leila Perie [aut]
Maintainer: Wenjie Sun <sunwjie at gmail.com>
citation("CellBarcode")):
Installation
To install this package, start R (version "4.2") 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")| 10X_Barcode | HTML | R Script |
| UMI_Barcode | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | CRISPR, Preprocessing, QualityControl, Sequencing, Software |
| Version | 1.4.0 |
| In Bioconductor since | BioC 3.14 (R-4.1) (2.5 years) |
| License | MIT + file LICENSE |
| 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, zlibbioc |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle, testthat (>= 3.0.0), knitr, rmarkdown |
| Linking To | Rcpp, 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_1.4.0.tar.gz |
| Windows Binary | CellBarcode_1.4.0.zip (64-bit only) |
| macOS Binary (x86_64) | CellBarcode_1.4.0.tgz |
| macOS Binary (arm64) | CellBarcode_1.4.0.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 |
| Old Source Packages for BioC 3.16 | Source Archive |