barbieQ
Analyze Barcode Data from Clonal Tracking Experiments
Bioconductor version: 3.24 · Package version: 1.5.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
The barbieQ package provides a series of robust statistical tools for analysing barcode count data generated from cell clonal tracking (i.e., lineage tracing) experiments. In these experiments, an initial cell and its offspring collectively form a clone (i.e., lineage). A unique barcode sequence, incorporated into the DNA of the inital cell, is inherited within the clone. This one-to-one mapping of barcodes to clones enables clonal tracking of their behaviors. By counting barcodes, researchers can quantify the population abundance of individual clones under specific experimental perturbations. barbieQ supports barcode count data preprocessing, statistical testing, and visualization.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("barbieQ")Details
| Maintainer | Liyang Fei <liyang.fei@petermac.org> |
| Author | Liyang Fei [aut, cre] (ORCID: <https://orcid.org/0000-0002-3293-2094>) |
| License | GPL-3 |
| URL | https://github.com/Oshlack/barbieQ/issues |
| Bug Reports | https://github.com/Oshlack/barbieQ |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Preprocessing, Regression, Sequencing, Software, Visualization |
| Package Short Url | https://bioconductor.org/packages/barbieQ/ |
Citation
From within R, enter citation("barbieQ"):
Liyang Fei. barbieQ: Analyze Barcode Data from Clonal Tracking Experiments. doi:10.18129/B9.bioc.barbieQ, R package version 1.5.0, https://bioconductor.org/packages/barbieQ.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | barbieQ_1.5.0.tar.gz |
| Windows binary (x86_64) | barbieQ_1.5.0.zip |
| macOS binary (arm64) | barbieQ_1.5.0.tgz |
| macOS binary (x86_64) | barbieQ_1.5.0.tgz |
Dependencies
Depends: R (>= 4.5)
Imports: magrittr, tidyr, dplyr, grid, circlize, ComplexHeatmap, ggplot2, logistf, limma, stats, igraph, utils, data.table, S4Vectors, SummarizedExperiment
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle