barcodetrackR

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see barcodetrackR.

Functions for Analyzing Cellular Barcoding Data

Bioconductor version: 3.21

barcodetrackR is an R package developed for the analysis and visualization of clonal tracking data. Data required is samples and tag abundances in matrix form. Usually from cellular barcoding experiments, integration site retrieval analyses, or similar technologies.

Author: Diego Alexander Espinoza [aut, cre], Ryland Mortlock [aut]

Maintainer: Diego Alexander Espinoza <diego.espinoza at pennmedicine.upenn.edu>

Citation (from within R, enter citation("barcodetrackR")):

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("barcodetrackR")

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("barcodetrackR")

barcodetrackR HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Sequencing, Software, Visualization

Version 1.16.0

In Bioconductor since BioC 3.13 (R-4.1) (4.5 years)

License file LICENSE

Depends R (>= 4.1)

Imports cowplot, circlize, dplyr, ggplot2, ggdendro, ggridges, graphics, grDevices, magrittr, plyr, proxy, RColorBrewer, rlang, scales, shiny, stats, SummarizedExperiment, S4Vectors, tibble, tidyr, vegan, viridis, utils

System Requirements

URL https://github.com/dunbarlabNIH/barcodetrackR

Suggests BiocStyle, knitr, magick, rmarkdown, testthat

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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package barcodetrackR_1.16.0.tar.gz

Windows Binary (x86_64) barcodetrackR_1.16.0.zip

macOS Binary (x86_64) barcodetrackR_1.16.0.tgz

macOS Binary (arm64) barcodetrackR_1.16.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/barcodetrackR

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/barcodetrackR

Bioc Package Browser https://code.bioconductor.org/browse/barcodetrackR/

Package Short Url https://bioconductor.org/packages/barcodetrackR/

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