Package: CGExplorer 0.3.2

CGExplorer: Chemo-Genomic Screening Data Preprocessor and Visualizer

An R package providing S4 data structures, analysis methods, and a Shiny application for preprocessing, quality control, and chemo-genomic interaction scoring of 384-well plate screening datasets generated by Tecan plate readers. Plate data is managed via a persistent local registry (PlateRegistry S4 object) that accumulates across sessions and survives package upgrades.

Authors:Qingzhou Zhang [aut, cre]

CGExplorer_0.3.2.tar.gz
CGExplorer_0.3.2.zip(r-4.7-any)CGExplorer_0.3.2.zip(r-4.6-any)CGExplorer_0.3.2.zip(r-4.5-any)
CGExplorer_0.3.2.tgz(r-4.6-any)CGExplorer_0.3.2.tgz(r-4.5-any)
CGExplorer_0.3.2.tar.gz(r-4.7-any)CGExplorer_0.3.2.tar.gz(r-4.6-any)
CGExplorer_0.3.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
CGExplorer/json (API)

# Install 'CGExplorer' in R:

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

Bug tracker:https://github.com/zqzneptune/cgexplorer/issues

On CRAN:

2.00 score 28 exports 93 dependencies

Last updated from:3abb4c5e72. Checks:7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel	NOTE	153
source / vignettes	OK	170
linux-release	NOTE	176
macos-release	NOTE	109
macos-oldrel	NOTE	109
windows-devel	NOTE	109
windows-release	NOTE	91
windows-oldrel	NOTE	93
wasm-release	OK	121

Exports:add_batch add_layout add_plate compute_relative_biofilm detect_staining_jump export_batch_growth_curves_pdf extract_biofilm_metrics extract_growth_metrics get_layout load_registry merge_plates new_batch new_plate new_registry parse_plate_layout parse_tecan_txt plot_multi_strain_growth_curves plot_plate_qc_layout plot_replicate_growth_curves remove_batch remove_layout remove_plate run_cgexplorer_app save_registry score_batch_dataset subtract_plate_blanks update_plate validate_batch_plates

Dependencies:askpass attempt base64enc bit bit64 bslib cachem cellranger cli clipr codetools commonmark config cpp11 crayon crosstalk curl data.table digest dplyr DT evaluate farver fastmap fontawesome fs generics ggplot2 glue golem gtable highr hms htmltools htmlwidgets httpuv httr isoband jquerylib jsonlite knitr labeling later lazyeval lifecycle lubridate magrittr memoise mime openssl otel pillar pkgconfig plotly prettyunits progress promises purrr R6 rappdirs RColorBrewer Rcpp readr readxl rematch rlang rmarkdown S7 sass scales shiny shinycssloaders shinydashboard shinyjs sourcetools stringi stringr sys tibble tidyr tidyselect timechange tinytex tzdb utf8 uuid vctrs viridisLite vroom withr xfun xtable yaml

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Add batch to registry	add_batch add_batch,PlateRegistry-method
Add layout to registry	add_layout add_layout,PlateRegistry-method
Add plate to registry	add_plate add_plate,PlateRegistry-method
S4 Class representing a Scoring Batch	Batch-class
S4 Generics for CGExplorer	CGExplorer-generics
Compute relative biofilm	compute_relative_biofilm
Detect staining addition from a kinetic read	detect_staining_jump
Export per-strain growth curves for a batch to a multi-page PDF	export_batch_growth_curves_pdf
Extract biofilm metrics	extract_biofilm_metrics
Extract growth metrics	extract_growth_metrics
Get layout from registry	get_layout get_layout,PlateRegistry-method
Load a PlateRegistry from RDS	load_registry
Merge plates in registry	merge_plates merge_plates,PlateRegistry-method
Constructor for Batch	new_batch
Constructor for Plate	new_plate
Constructor for PlateRegistry	new_registry
Parse 96 or 384 well Plate Layout	parse_plate_layout
Parse Tecan Plate Reader output (.txt)	parse_tecan_txt
S4 Class representing a Chemo-Genomic Plate	Plate-class
S4 Class representing the Project Plate Registry	PlateRegistry-class
Plot Multi-Strain Growth Curves	plot_multi_strain_growth_curves
Plot Plate QC Layout	plot_plate_qc_layout
Plot Replicate Growth Curves	plot_replicate_growth_curves
Remove batch from registry	remove_batch remove_batch,PlateRegistry-method
Remove layout from registry	remove_layout remove_layout,PlateRegistry-method
Remove plate from registry	remove_plate remove_plate,PlateRegistry-method
Run the Shiny Application	run_cgexplorer_app
Save registry to disk	save_registry save_registry,PlateRegistry-method
Standardized Scoring Engine	score_batch_dataset
Subtract blanks at the plate level	subtract_plate_blanks
Update plate in registry	update_plate update_plate,PlateRegistry-method
Validate plate eligibility and layout uniformity for a batch	validate_batch_plates