Package: barcodetrackR 1.15.0

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]

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barcodetrackR.pdf |barcodetrackR.html✨
barcodetrackR/json (API)
NEWS

# Install 'barcodetrackR' in R:

install.packages('barcodetrackR', repos = c('https://bioc.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 BioConductor:barcodetrackR-1.15.0(bioc 3.21)barcodetrackR-1.14.0(bioc 3.20)

software visualization sequencing

4.70 score 5 stars 6 scripts 253 downloads 25 exports 94 dependencies

Last updated 22 days agofrom:c0c5333d0d. Checks:OK: 1 WARNING: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 19 2024
R-4.5-win	WARNING	Nov 19 2024
R-4.5-linux	WARNING	Nov 19 2024
R-4.4-win	WARNING	Nov 19 2024
R-4.4-mac	WARNING	Nov 19 2024
R-4.3-win	WARNING	Nov 19 2024
R-4.3-mac	WARNING	Nov 19 2024

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

barcodetrackR

Diego A. Espinoza & Ryland D. Mortlock

Rendered fromIntroduction_to_barcodetrackR.Rmdusingknitr::rmarkdownon Nov 19 2024.

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