barbieQ
This is the released version of barbieQ; for the devel version, see barbieQ.
Analyze Barcode Data from Clonal Tracking Experiments
Bioconductor version: Release (3.23)
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.
Maintainer: Liyang Fei <liyang.fei at petermac.org>
citation("barbieQ")):Liyang Fei. barbieQ: Analyze Barcode Data from Clonal Tracking Experiments. doi:10.18129/B9.bioc.barbieQ, R package version 1.4.0, https://bioconductor.org/packages/barbieQ.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("barbieQ")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("barbieQ")| Quick start to barbieQ | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Preprocessing, Regression, Sequencing, Software, Visualization |
| Version | 1.4.0 |
| In Bioconductor since | BioC 3.21 (R-4.5) (1.5 years) |
| License | GPL-3 |
| Depends | R (>= 4.5) |
| Imports | magrittr, tidyr, dplyr, grid, circlize, ComplexHeatmap, ggplot2, logistf, limma, stats, igraph, utils, data.table, S4Vectors, SummarizedExperiment |
| System Requirements | |
| URL | https://github.com/Oshlack/barbieQ/issues |
| Bug Reports | https://github.com/Oshlack/barbieQ |
See More
| Suggests | knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | barbieQ_1.4.0.tar.gz |
| Windows Binary (x86_64) | barbieQ_1.4.0.zip |
| macOS Binary (big-sur-x86_64) | barbieQ_1.4.0.tgz |
| macOS Binary (sonoma-arm64) | barbieQ_1.4.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/barbieQ |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/barbieQ |
| Package Short Url | https://bioconductor.org/packages/barbieQ/ |
| Package Downloads Report | Download Stats |