Package: CRISPRball 1.1.0

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_1.1.0.tar.gz
CRISPRball_1.1.0.zip(r-4.5)CRISPRball_1.1.0.zip(r-4.4)CRISPRball_1.1.0.zip(r-4.3)
CRISPRball_1.1.0.tgz(r-4.4-any)CRISPRball_1.1.0.tgz(r-4.3-any)
CRISPRball_1.1.0.tar.gz(r-4.5-noble)CRISPRball_1.1.0.tar.gz(r-4.4-noble)
CRISPRball_1.1.0.tgz(r-4.4-emscripten)CRISPRball_1.1.0.tgz(r-4.3-emscripten)
CRISPRball.pdf |CRISPRball.html✨
CRISPRball/json (API)
NEWS

# 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_TPM - DepMap expression data
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

On BioConductor:CRISPRball-1.1.0(bioc 3.20)CRISPRball-1.0.0(bioc 3.19)

bioconductor-package

17 exports 1.00 score 211 dependencies

Last updated 2 months agofrom:429fdab2d8

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 AnnotationDbi AnnotationHub anytime ape aplot askpass babelgene base64enc beachmat BH Biobase BiocFileCache BiocGenerics BiocManager BiocParallel BiocSingular BiocVersion Biostrings bit bit64 bitops blob bslib cachem circlize cli clisymbols clue cluster clusterProfiler codetools colorspace colourpicker commonmark ComplexHeatmap cowplot cpp11 crayon crosstalk curl data.table DBI dbplyr DelayedArray DelayedMatrixStats depmap digest dittoSeq doParallel DOSE downloader dplyr dqrng DT enrichplot evaluate ExperimentHub fansi farver fastmap fastmatch fgsea filelock fontawesome foreach formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges GetoptLong ggforce ggfun ggnewscale ggplot2 ggplotify ggraph ggrepel ggridges ggtree GlobalOptions glue GO.db GOSemSim graph graphlayouts gridExtra gridGraphics gson gtable HDO.db highr htmltools htmlwidgets httpuv httr httr2 igraph InteractiveComplexHeatmap IRanges irlba isoband iterators jquerylib jsonlite kableExtra KEGGgraph KEGGREST knitr labeling lambda.r later lattice lazyeval lifecycle MAGeCKFlute magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime miniUI msigdbr munsell nlme openssl org.Hs.eg.db patchwork pathview PCAtools pheatmap pillar pkgconfig plogr plotly plyr png polyclip promises purrr qvalue R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen RCurl reshape2 Rgraphviz rjson rlang rmarkdown RSQLite rstudioapi rsvd S4Arrays S4Vectors sass ScaledMatrix scales scatterpie shadowtext shape shiny shinyBS shinycssloaders shinyjqui shinyjs shinyWidgets SingleCellExperiment sitmo snow sourcetools SparseArray sparseMatrixStats stringi stringr SummarizedExperiment svglite sys systemfonts tibble tidygraph tidyr tidyselect tidytree tinytex treeio tweenr UCSC.utils utf8 vctrs viridis viridisLite withr xfun XML xml2 xtable XVector yaml yulab.utils zlibbioc

CRISPRball Quick Start

Jared Andrews

Rendered fromCRISPRball.Rmdusingknitr::rmarkdownon Jun 30 2024.

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