Package: cellGeometry 0.6.4

cellGeometry: Geometric Single Cell Deconvolution

Deconvolution of bulk RNA-Sequencing data into proportions of cells based on a reference single-cell RNA-Sequencing dataset using high-dimensional geometric methodology <doi:10.1038/s41467-026-75762-7>.

Authors:Myles Lewis [aut, cre], Rachel Lau [ctb]

cellGeometry_0.6.4.tar.gz
cellGeometry_0.6.4.zip(r-4.7-any)cellGeometry_0.6.4.zip(r-4.6-any)cellGeometry_0.6.4.zip(r-4.5-any)
cellGeometry_0.6.4.tgz(r-4.6-any)cellGeometry_0.6.4.tgz(r-4.5-any)
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cellGeometry_0.6.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
cellGeometry/json (API)

# Install 'cellGeometry' in R:
install.packages('cellGeometry', repos = c('https://myles-lewis.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/myles-lewis/cellgeometry/issues

On CRAN:

Conda:

7.16 score 20 stars 48 scripts 658 downloads 46 exports 104 dependencies

Last updated from:fcabe0d2a5. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK359
source / vignettesOK248
linux-releaseOK379
macos-releaseOK259
macos-oldrelOK241
windows-develOK318
windows-releaseOK302
windows-oldrelOK365
wasm-releaseOK160

Exports:add_noiseadjust_library_sizecellMarkerscollapse_groupcomp_heatmapcos_similaritydeconvolutediagnosefix_bulkfix_groupgene_anglegene2symbolgenerate_samplesggplot_residualsgraded_log_noiselog_noiselogmeanmax_similaritymergeMarkersmetric_setplot_biasvarplot_compplot_cvplot_predplot_residualsplot_setplot_tunequantile_maprank_anglereduceNoisescapplyscmeanseshift_noisesignature_heatmapsimulate_bulkslapplyspecificity_plotspecificity_plotlyspillover_heatmapsqrt_noisestack_ggplotstack_plottune_deconvupdateMarkersviolin_plot

Dependencies:abindAnnotationDbiAnnotationFilteraskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobcachemcigarillocirclizecliclueclustercodetoolscolorspaceComplexHeatmapcpp11crayoncurlDBIDelayedArraydigestdoParalleldplyrensembldbfarverfastmapforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesGetoptLongggplot2ggrepelGlobalOptionsgluegtablegtoolshttrIRangesisobanditeratorsjsonliteKEGGRESTlabelinglambda.rlatticelazyevallifecyclemagrittrMatrixMatrixGenericsmatrixStatsmcprogressmemoisemimeopensslpillarpkgconfigpngProtGenericsR6RColorBrewerRcppRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsS7scalesSeqinfoshapesnowSparseArraysystibbletidyselectUCSC.utilsutf8vctrsviridisLitewithrXMLXVectoryaml

cellGeometry quickstart
Geometric single cell deconvolution | Installation | Algorithm | Example dataset | h5ad file | Seurat file | Obtain gene signatures | Extract cell clusters | Create gene signature | Visualise gene signature | Signature diagnostics | Refine gene signature | Deconvolution | Sampled pseudo-bulk | Real bulk RNA-Seq settings | Tuning deconvolution | Simulating noise | Deconvolution diagnostics | Standard error | Confidence intervals | Residual gene expression | Multipass outlying gene removal | Variable compensation | Citation
Rendered fromintro.Rmdusingknitr::rmarkdown

Last update: 2026-08-26
Started: 2025-02-17

Brain atlas deconvolution
Brain Atlas | Neurons | Non-neuronal cells | Merging signatures | Simulating pseudobulk | Merging simulated data | Deconvolution
Rendered frombrain_atlas.Rmdusingknitr::rmarkdown

Last update: 2026-01-23
Started: 2025-06-05

Readme and manuals

Help Manual

Help pageTopics
Add noise to count dataadd_noise graded_log_noise log_noise shift_noise sqrt_noise
Adjust count matrix by library sizeadjust_library_size
Identify cell markerscellMarkers
Collapse groups in cellMarkers objectcollapse_group
Compensation heatmapcomp_heatmap
Confidence Intervals for Deconvolution Modelsconfint.deconv
Gene signature cosine similarity matrixcos_similarity
Deconvolute bulk RNA-Seq using single-cell RNA-Seq signaturedeconvolute
Diagnostics for cellMarker signaturesdiagnose
Fix in missing genes in bulk RNA-Seq matrixfix_bulk
Fix cellMarkers signature with no cell groupsfix_group
Vector based best marker selectiongene_angle
Converts ensembl gene ids to symbolsgene2symbol
Generate random cell number samplesgenerate_samples
Compute condition number of deconvolution modelkappa.deconv
Mean Objectslog2s logmean trimmean
Maximum similarity between cell typesmax_similarity
Merge cellMarker signaturesmergeMarkers
Calculate R-squared and metrics on deconvoluted cell subclassesmetric_set
Plot bias-variance decompositionplot_biasvar
Plot compensation analysisplot_comp plot_path
Plot deconvolution lambda cross-validation curveplot_cv
Scatter plot to compare deconvoluted subclassesplot_pred
Residuals plotggplot_residuals plot_residuals
Scatter plots to compare deconvoluted subclassesplot_set
Plot tuning curvesplot_tune
Quantile-quantile plotplot.qqmap
Quantile mapping function between two scRNA-Seq datasetsquantile_map
Rank distance angles from a cosine similarity matrixrank_angle
Reduce noise in single-cell datareduceNoise
Extract Deconvolution Residualsresiduals.deconv
Regression Deletion Diagnosticscooks.distance.deconv rstandard.deconv rstudent.deconv
Single-cell apply a function to a matrix split by a factorscapply
Single-cell mean log gene expression across cell typesscmean
Standard errors of deconvoluted cell countsse
Gene signature heatmapsignature_heatmap
Simulate pseudo-bulk RNA-Seqsimulate_bulk
Apply a function to a big matrix by slicingslapply
Specificity plotspecificity_plot specificity_plotly
Spillover heatmapspillover_heatmap
Stacked bar plotstack_ggplot stack_plot
Summarising deconvolution tuningsummary.tune_deconv
Tune deconvolution parameterstune_deconv
Update cellMarkers objectupdateMarkers
Cell subclass violin plotviolin_plot