Package: CRISPRball 1.9.0

Jared Andrews

CRISPRball: Shiny Application for Interactive CRISPR Screen Visualization, Exploration, Comparison, and Filtering

A Shiny application for visualization, exploration, comparison, and filtering of CRISPR screens analyzed with MAGeCK RRA or MLE. Features include interactive plots with on-click labeling, full customization of plot aesthetics, data upload and/or download, and much more. Quickly and easily explore your CRISPR screen results and generate publication-quality figures in seconds.

Authors:Jared Andrews [aut, cre], Jacob Steele [ctb]

CRISPRball_1.9.0.tar.gz
CRISPRball_1.9.0.zip(r-4.7)CRISPRball_1.9.0.zip(r-4.6)CRISPRball_1.9.0.zip(r-4.5)
CRISPRball_1.9.0.tgz(r-4.6-any)CRISPRball_1.9.0.tgz(r-4.5-any)
CRISPRball_1.9.0.tar.gz(r-4.7-any)CRISPRball_1.9.0.tar.gz(r-4.6-any)
CRISPRball_1.9.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
CRISPRball/json (API)

# Install 'CRISPRball' in R:

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

Bug tracker:https://github.com/j-andrews7/crisprball/issues

Datasets:

depmap_22q1_cn - DepMap copy number data
depmap_22q1_crispr - DepMap CRISPR screen data
depmap_22q1_crispr_rnai - DepMap CRISPR & RNAi screen data
depmap_22q1_rnai - DepMap RNAi screen data
depmap_22q1_TPM - DepMap expression data

On BioConductor:CRISPRball-1.9.0(bioc 3.24)CRISPRball-1.8.0(bioc 3.23)

software shinyapps crispr qualitycontrol visualization gui crispr-screen data-visualization interactive-visualizations mageck plotly screening shiny

5.80 score 13 stars 24 scripts 255 downloads 17 exports 143 dependencies

Last updated from:8bce8d88c9. Checks:8 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	252
linux-devel-x86_64	NOTE	460
source / vignettes	OK	351
linux-release-x86_64	NOTE	444
macos-release-arm64	NOTE	309
macos-oldrel-arm64	NOTE	301
windows-devel	NOTE	388
windows-release	NOTE	383
windows-oldrel	NOTE	381
wasm-release	OK	209

Exports:build_depmap_db CRISPRball gene_ingress get_depmap_essentiality get_depmap_plot_data plot_bar plot_correlation_heatmap plot_depmap_cn plot_depmap_dependency plot_depmap_expression plot_depmap_lineages plot_hist plot_lawn plot_pca_biplot plot_rank plot_volcano read_mle_gene_summary

Dependencies:abind askpass assorthead base64enc beachmat BH Biobase BiocGenerics BiocParallel BiocSingular bslib cachem circlize cli clisymbols clue cluster codetools colorspace colourpicker commonmark ComplexHeatmap cowplot cpp11 crayon crosstalk curl data.table DelayedArray DelayedMatrixStats digest dittoSeq doParallel dplyr dqrng DT evaluate farver fastmap fontawesome foreach formatR fs futile.logger futile.options generics GenomicRanges GetoptLong ggplot2 ggrepel ggridges GlobalOptions glue gridExtra gtable highr htmltools htmlwidgets httpuv httr InteractiveComplexHeatmap IRanges irlba isoband iterators jquerylib jsonlite kableExtra knitr labeling lambda.r later lattice lazyeval lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime miniUI openssl otel PCAtools pheatmap pillar pkgconfig plotly plyr png promises purrr R6 rappdirs RColorBrewer Rcpp reshape2 rjson rlang rmarkdown rstudioapi rsvd S4Arrays S4Vectors S7 sass ScaledMatrix scales Seqinfo shape shiny shinyBS shinycssloaders shinyjqui shinyjs shinyWidgets SingleCellExperiment sitmo snow sourcetools SparseArray sparseMatrixStats stringi stringr SummarizedExperiment svglite sys systemfonts textshaping tibble tidyr tidyselect tinytex utf8 vctrs viridisLite withr xfun xml2 xtable XVector yaml

CRISPRball Quick Start

Rendered fromCRISPRball.Rmdusingknitr::rmarkdown

Last update: 2023-10-18
Started: 2022-05-03

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Build SQLite database of DepMap data	build_depmap_db
Create an interactive Shiny app for visualization & exploration of CRISPR analyses	CRISPRball
DepMap copy number data	depmap_22q1_cn
DepMap CRISPR screen data	depmap_22q1_crispr
DepMap CRISPR & RNAi screen data	depmap_22q1_crispr_rnai
DepMap RNAi screen data	depmap_22q1_rnai
DepMap expression data	depmap_22q1_TPM
Parse gene summary data for easier plotting and display	gene_ingress
Get essential/selective gene information from DepMap summary table.	get_depmap_essentiality
Create DepMap dataframe for plotting	get_depmap_plot_data
Create interactive bar plot	plot_bar
Plot a Correlation Heatmap	plot_correlation_heatmap
Plot gene copy number information from DepMap	plot_depmap_cn
Plot gene dependency information from DepMap CRISPR and RNAi tables	plot_depmap_dependency
Plot gene expression information from DepMap, mostly from CCLE	plot_depmap_expression
Plot selected information across lineages from DepMap.	plot_depmap_lineages
Create a plotly plot from a distribution of values	plot_hist
Create an interactive lawn plot	plot_lawn
Plot a biplot from a PCAtools 'pca' object	plot_pca_biplot
Create an interactive rank plot	plot_rank
Create an interactive volcano plot	plot_volcano
Read and parse MAGeCK MLE output gene summary file	read_mle_gene_summary