Package: chevreulPlot 0.99.34

Kevin Stachelek

chevreulPlot: Plots used in the chevreulPlot package

Tools for plotting SingleCellExperiment objects in the chevreulPlot package. Includes functions for analysis and visualization of single-cell data. Supported by NIH grants R01CA137124 and R01EY026661 to David Cobrinik.

Authors:Kevin Stachelek [aut, cre], Bhavana Bhat [aut]

chevreulPlot_0.99.34.tar.gz
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chevreulPlot.pdf |chevreulPlot.html✨
chevreulPlot/json (API)
NEWS

# Install 'chevreulPlot' in R:

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

Bug tracker:https://github.com/cobriniklab/chevreulplot/issues

Datasets:

cc.genes.cyclone - Cyclone cell cycle pairs by symbol
ensembl_version - Ensembl version used for build
grch38 - Human annotation data
grch38_tx2gene - Human transcripts to genes
human_to_mouse_homologs - Gene Homologs Between Human and Mouse
small_example_dataset - Small example SingleCellExperiment
tiny_sce - Tiny example SingleCellExperiment

On BioConductor:chevreulPlot-0.99.32(bioc 3.21)

coverage rnaseq sequencing visualization geneexpression transcription singlecell transcriptomics normalization preprocessing qualitycontrol dimensionreduction dataimport

5.08 score 2 scripts 8 exports 224 dependencies

Last updated 11 days agofrom:5e39a4d320. Checks:1 OK, 5 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Feb 28 2025
R-4.5-win	NOTE	Feb 28 2025
R-4.5-mac	NOTE	Feb 28 2025
R-4.5-linux	NOTE	Feb 28 2025
R-4.4-win	NOTE	Feb 28 2025
R-4.4-mac	NOTE	Feb 28 2025

Exports:make_complex_heatmap plot_all_transcripts plot_colData_histogram plot_colData_on_embedding plot_feature_on_embedding plot_marker_features plot_transcript_composition plot_violin

Dependencies:abind AnnotationDbi AnnotationFilter askpass assertthat assorthead backports base64enc batchelor beachmat beeswarm BH Biobase BiocGenerics BiocIO BiocNeighbors BiocParallel BiocSingular Biostrings bit bit64 bitops blob bluster brio bslib cachem Cairo callr checkmate chevreulProcess circlize cli clipr clue cluster clustree cmdfun codetools colorspace ComplexHeatmap cowplot cpp11 crayon credentials crosstalk curl data.table DBI DelayedArray DelayedMatrixStats desc diffobj digest doParallel dplyr dqrng edgeR EnsDb.Hsapiens.v86 ensembldb evaluate fansi farver fastmap FNN fontawesome forcats foreach formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges gert GetoptLong ggbeeswarm ggforce ggplot2 ggraph ggrastr ggrepel gh gitcreds GlobalOptions glue graphlayouts gridExtra gtable highr hms htmltools htmlwidgets httr httr2 igraph ini IRanges irlba isoband iterators jquerylib jsonlite KEGGREST knitr labeling lambda.r later lattice lazyeval lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats megadepth memoise metapod mgcv mime munsell nlme openssl patchwork pheatmap pillar pkgbuild pkgconfig pkgload plogr plotly png polyclip praise prettyunits processx progress promises ProtGenerics ps purrr R.methodsS3 R.oo R.utils R6 ragg rappdirs RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppML RcppProgress RCurl readr ResidualMatrix restfulr Rhtslib rjson rlang rmarkdown rprojroot Rsamtools RSpectra RSQLite rstudioapi rsvd rtracklayer Rtsne S4Arrays S4Vectors sass ScaledMatrix scales scater scran scuttle shape SingleCellExperiment sitmo snow SparseArray sparseMatrixStats statmod stringi stringr SummarizedExperiment sys systemfonts testthat textshaping tibble tidygraph tidyr tidyselect tinytex tweenr tzdb UCSC.utils usethis utf8 uwot vctrs vipor viridis viridisLite vroom waldo whisker wiggleplotr withr xfun XML XVector yaml zip

Chevreul

Kevin Stachelek, Bhavana Bhat

Rendered fromchevreulPlot.Rmdusingknitr::rmarkdownon Feb 28 2025.

Last update: 2025-02-11
Started: 2024-10-23

Visualization

Kevin Stachelek, Bhavana Bhat

Rendered fromvisualization.Rmdusingknitr::rmarkdownon Feb 28 2025.

Last update: 2025-02-11
Started: 2024-10-23

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Cyclone cell cycle pairs by symbol	cc.genes.cyclone
Enframe Cluster Markers	enframe_markers
Ensembl version used for build	ensembl_version
Human annotation data	grch38
Human transcripts to genes	grch38_tx2gene
Gene Homologs Between Human and Mouse	human_to_mouse_homologs
Plot Annotated Complexheatmap from SingleCellExperiment object	make_complex_heatmap
Plot All Transcripts	plot_all_transcripts
Plot Read Count	plot_colData_histogram
Plot Metadata Variables	plot_colData_on_embedding
Plot Feature	plot_feature_on_embedding
Plot BigWig Coverage for Genes of Interest by a Given Variable	plot_gene_coverage_by_var
Plot Cluster Marker Genes	plot_marker_features
Plot Transcript Composition	plot_transcript_composition
Plot Violin plot	plot_violin
Plotly settings	plotly_settings
Small example SingleCellExperiment	small_example_dataset
Tiny example SingleCellExperiment	tiny_sce