Package: barcodetrackR 1.20.0

Diego Alexander Espinoza

barcodetrackR: Functions for Analyzing Cellular Barcoding Data

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.

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

barcodetrackR_1.20.0.tar.gz
barcodetrackR_1.20.0.zip(r-4.7)barcodetrackR_1.20.0.zip(r-4.6)barcodetrackR_1.20.0.zip(r-4.5)
barcodetrackR_1.20.0.tgz(r-4.6-any)barcodetrackR_1.20.0.tgz(r-4.5-any)
barcodetrackR_1.20.0.tar.gz(r-4.7-any)barcodetrackR_1.20.0.tar.gz(r-4.6-any)
barcodetrackR_1.20.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
barcodetrackR/json (API)
NEWS

# Install 'barcodetrackR' in R:

install.packages('barcodetrackR', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/dunbarlabnih/barcodetrackr/issues

Datasets:

wu_subset - Small subset of Wu barcoding dataset

On CRAN:

software visualization sequencing

3.88 score 5 stars 10 scripts 330 downloads 25 exports 85 dependencies

Last updated from:0735f99f0d (on RELEASE_3_23). Checks:1 WARNING, 7 ERROR, 2 OK. Indexed: no.

Target	Result	Time
bioc-checks	WARNING	181
linux-devel-x86_64	ERROR	354
source / vignettes	OK	269
linux-release-x86_64	ERROR	306
macos-release-arm64	ERROR	364
macos-oldrel-arm64	ERROR	203
windows-devel	ERROR	243
windows-release	ERROR	287
windows-oldrel	ERROR	232
wasm-release	OK	134

Exports:barcode_binary_heatmap barcode_ggheatmap barcode_ggheatmap_stat barcode_stat_test bias_histogram bias_lineplot bias_ridge_plot chord_diagram clonal_contribution clonal_count clonal_diversity cor_plot create_SE dist_plot estimate_barcode_threshold get_top_clones launchApp mds_plot rank_abundance_plot rank_abundance_stat_test scatter_plot stat_hist subset_SE threshold threshold_SE

Dependencies:abind base64enc Biobase BiocGenerics bslib cachem circlize cli cluster colorspace commonmark cowplot cpp11 DelayedArray digest dplyr farver fastmap fontawesome fs generics GenomicRanges ggdendro ggplot2 ggridges GlobalOptions glue gridExtra gtable htmltools httpuv IRanges isoband jquerylib jsonlite labeling later lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime nlme otel permute pillar pkgconfig plyr promises proxy purrr R6 rappdirs RColorBrewer Rcpp rlang S4Arrays S4Vectors S7 sass scales Seqinfo shape shiny sourcetools SparseArray stringi stringr SummarizedExperiment tibble tidyr tidyselect utf8 vctrs vegan viridis viridisLite withr xtable XVector

barcodetrackR

Diego A. Espinoza & Ryland D. Mortlock

Rendered fromIntroduction_to_barcodetrackR.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2021-04-04
Started: 2020-02-24

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Barcode Binary Heatmap	barcode_binary_heatmap
barcode_ggheatmap	barcode_ggheatmap
Barcode Top Clone Heatmap	barcode_ggheatmap_stat
Barcode Statistical Test	barcode_stat_test
Bias histogram	bias_histogram
Bias line plot	bias_lineplot
Bias Ridge plot	bias_ridge_plot
Build html	build_index_html
Barcode Chord Diagram	chord_diagram
Clonal contribution plot	clonal_contribution
Clonal count plot	clonal_count
Clonal diversity plot	clonal_diversity
Correlation Plot	cor_plot
create_SE	create_SE
Pairwise Distance Plot	dist_plot
Estimate Barcode Threshold	estimate_barcode_threshold
get_top_clones (helper function)	get_top_clones
Launch Barcode App	launchApp
MDS Plot	mds_plot
Rank Abundance Plot	rank_abundance_plot
Rank Abundance Statistical Test	rank_abundance_stat_test
Scatter Plot	scatter_plot
Stat histogram	stat_hist
subset_SE	subset_SE
Threshold	threshold
Threshold SE	threshold_SE
Small subset of Wu barcoding dataset	wu_subset