Package: chevreulPlot 0.99.34
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:
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
- 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)
coveragernaseqsequencingvisualizationgeneexpressiontranscriptionsinglecelltranscriptomicsnormalizationpreprocessingqualitycontroldimensionreductiondataimport
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_heatmapplot_all_transcriptsplot_colData_histogramplot_colData_on_embeddingplot_feature_on_embeddingplot_marker_featuresplot_transcript_compositionplot_violin
Dependencies:abindAnnotationDbiAnnotationFilteraskpassassertthatassortheadbackportsbase64encbatchelorbeachmatbeeswarmBHBiobaseBiocGenericsBiocIOBiocNeighborsBiocParallelBiocSingularBiostringsbitbit64bitopsblobblusterbriobslibcachemCairocallrcheckmatechevreulProcesscirclizeclicliprclueclusterclustreecmdfuncodetoolscolorspaceComplexHeatmapcowplotcpp11crayoncredentialscrosstalkcurldata.tableDBIDelayedArrayDelayedMatrixStatsdescdiffobjdigestdoParalleldplyrdqrngedgeREnsDb.Hsapiens.v86ensembldbevaluatefansifarverfastmapFNNfontawesomeforcatsforeachformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesgertGetoptLongggbeeswarmggforceggplot2ggraphggrastrggrepelghgitcredsGlobalOptionsgluegraphlayoutsgridExtragtablehighrhmshtmltoolshtmlwidgetshttrhttr2igraphiniIRangesirlbaisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmegadepthmemoisemetapodmgcvmimemunsellnlmeopensslpatchworkpheatmappillarpkgbuildpkgconfigpkgloadplogrplotlypngpolyclippraiseprettyunitsprocessxprogresspromisesProtGenericspspurrrR.methodsS3R.ooR.utilsR6raggrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppMLRcppProgressRCurlreadrResidualMatrixrestfulrRhtslibrjsonrlangrmarkdownrprojrootRsamtoolsRSpectraRSQLiterstudioapirsvdrtracklayerRtsneS4ArraysS4VectorssassScaledMatrixscalesscaterscranscuttleshapeSingleCellExperimentsitmosnowSparseArraysparseMatrixStatsstatmodstringistringrSummarizedExperimentsyssystemfontstestthattextshapingtibbletidygraphtidyrtidyselecttinytextweenrtzdbUCSC.utilsusethisutf8uwotvctrsviporviridisviridisLitevroomwaldowhiskerwiggleplotrwithrxfunXMLXVectoryamlzip
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 |