Package: cellGeometry 0.6.3

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:10.64898/2026.01.24.701240>.

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

cellGeometry_0.6.3.tar.gz
cellGeometry_0.6.3.zip(r-4.7)cellGeometry_0.6.3.zip(r-4.6)cellGeometry_0.6.3.zip(r-4.5)
cellGeometry_0.6.3.tgz(r-4.6-any)cellGeometry_0.6.3.tgz(r-4.5-any)
cellGeometry_0.6.3.tar.gz(r-4.7-any)cellGeometry_0.6.3.tar.gz(r-4.6-any)
cellGeometry_0.6.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
cellGeometry/json (API)
NEWS

# 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:

7.57 score 14 stars 49 scripts 2.0k downloads 46 exports 105 dependencies

Last updated from:83c826ae9d. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	452
source / vignettes	OK	328
linux-release-x86_64	OK	391
macos-release-arm64	OK	378
macos-oldrel-arm64	OK	289
windows-devel	OK	306
windows-release	OK	390
windows-oldrel	OK	310
wasm-release	OK	177

Exports:add_noise adjust_library_size cellMarkers collapse_group comp_heatmap cos_similarity deconvolute diagnose fix_bulk fix_group gene_angle gene2symbol generate_samples ggplot_residuals graded_log_noise log_noise logmean max_similarity mergeMarkers metric_set plot_biasvar plot_comp plot_cv plot_pred plot_residuals plot_set plot_tune quantile_map rank_angle reduceNoise scapply scmean se shift_noise signature_heatmap simulate_bulk slapply specificity_plot specificity_plotly spillover_heatmap sqrt_noise stack_ggplot stack_plot tune_deconv updateMarkers violin_plot

Dependencies:abind AnnotationDbi AnnotationFilter askpass BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob cachem cigarillo circlize cli clue cluster codetools colorspace ComplexHeatmap cpp11 crayon curl DBI DelayedArray digest doParallel dplyr ensembldb farver fastmap foreach formatR futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GetoptLong ggplot2 ggrepel GlobalOptions glue gtable gtools httr IRanges isoband iterators jsonlite KEGGREST labeling lambda.r lattice lazyeval lifecycle magrittr Matrix MatrixGenerics matrixStats mcprogress memoise mime openssl pillar pkgconfig png ProtGenerics R6 RColorBrewer Rcpp RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors S7 scales Seqinfo shape snow SparseArray SummarizedExperiment sys tibble tidyselect UCSC.utils utf8 vctrs viridisLite withr XML XVector yaml

cellGeometry quickstart

Myles Lewis

Rendered fromintro.Rmdusingknitr::rmarkdownon May 19 2026.

Last update: 2026-04-18
Started: 2025-02-17

Brain atlas deconvolution

Myles Lewis

Rendered frombrain_atlas.Rmdusingknitr::rmarkdownon May 19 2026.

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Add noise to count data	add_noise graded_log_noise log_noise shift_noise sqrt_noise
Adjust count matrix by library size	adjust_library_size
Identify cell markers	cellMarkers
Collapse groups in cellMarkers object	collapse_group
Compensation heatmap	comp_heatmap
Confidence Intervals for Deconvolution Models	confint.deconv
Gene signature cosine similarity matrix	cos_similarity
Deconvolute bulk RNA-Seq using single-cell RNA-Seq signature	deconvolute
Diagnostics for cellMarker signatures	diagnose
Fix in missing genes in bulk RNA-Seq matrix	fix_bulk
Fix cellMarkers signature with no cell groups	fix_group
Vector based best marker selection	gene_angle
Converts ensembl gene ids to symbols	gene2symbol
Generate random cell number samples	generate_samples
Compute condition number of deconvolution model	kappa.deconv
Mean Objects	log2s logmean trimmean
Maximum similarity between cell types	max_similarity
Merge cellMarker signatures	mergeMarkers
Calculate R-squared and metrics on deconvoluted cell subclasses	metric_set
Plot bias-variance decomposition	plot_biasvar
Plot compensation analysis	plot_comp plot_path
Plot deconvolution lambda cross-validation curve	plot_cv
Scatter plot to compare deconvoluted subclasses	plot_pred
Residuals plot	ggplot_residuals plot_residuals
Scatter plots to compare deconvoluted subclasses	plot_set
Plot tuning curves	plot_tune
Quantile-quantile plot	plot.qqmap
Quantile mapping function between two scRNA-Seq datasets	quantile_map
Rank distance angles from a cosine similarity matrix	rank_angle
Reduce noise in single-cell data	reduceNoise
Extract Deconvolution Residuals	residuals.deconv
Regression Deletion Diagnostics	cooks.distance.deconv rstandard.deconv rstudent.deconv
Single-cell apply a function to a matrix split by a factor	scapply
Single-cell mean log gene expression across cell types	scmean
Standard errors of deconvoluted cell counts	se
Gene signature heatmap	signature_heatmap
Simulate pseudo-bulk RNA-Seq	simulate_bulk
Apply a function to a big matrix by slicing	slapply
Specificity plot	specificity_plot specificity_plotly
Spillover heatmap	spillover_heatmap
Stacked bar plot	stack_ggplot stack_plot
Summarising deconvolution tuning	summary.tune_deconv
Tune deconvolution parameters	tune_deconv
Update cellMarkers object	updateMarkers
Cell subclass violin plot	violin_plot