- Home
- Bioconductor 3.22
- Software Packages
- CellBarcode
CellBarcode
This is thereleased version of CellBarcode; for the devel version, seeCellBarcode.
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("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 appropriateBioconductor 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 |
Details
| biocViews | CRISPR,Preprocessing,QualityControl,Sequencing,Software |
| Version | 1.16.0 |
| In Bioconductor since | BioC 3.14 (R-4.1) (4 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 |
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
FollowInstallation instructions to use this package in your R session.
| Source Package | CellBarcode_1.16.0.tar.gz |
| Windows Binary (x86_64) | CellBarcode_1.16.0.zip |
| macOS Binary (x86_64) | CellBarcode_1.16.0.tgz |
| macOS Binary (arm64) | CellBarcode_1.16.0.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 |