CellBarcode
This is the released version of CellBarcode; for the devel version, see CellBarcode.
Cellular DNA Barcode Analysis toolkit
Bioconductor version: Release (3.23)
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]
, Anne-Marie Lyne [aut], Leila Perie [aut]
Maintainer: Wenjie Sun <sunwjie at gmail.com>
citation("CellBarcode")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 |
Details
| biocViews | CRISPR, Preprocessing, QualityControl, Sequencing, Software |
| Version | 1.18.0 |
| In Bioconductor since | BioC 3.14 (R-4.1) (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 |
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_1.18.0.tar.gz |
| Windows Binary (x86_64) | CellBarcode_1.18.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | CellBarcode_1.18.0.tgz |
| macOS Binary (sonoma-arm64) | CellBarcode_1.18.0.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 |