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barcodetrackR

Functions for Analyzing Cellular Barcoding Data


Bioconductor version: Release (3.18)

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 "4.3") 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

Details

biocViews Sequencing, Software, Visualization
Version 1.10.0
In Bioconductor since BioC 3.13 (R-4.1) (3 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
See More
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_1.10.0.tar.gz
Windows Binary barcodetrackR_1.10.0.zip
macOS Binary (x86_64) barcodetrackR_1.10.0.tgz
macOS Binary (arm64) barcodetrackR_1.10.0.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/
Package Downloads Report Download Stats