Geometric Single Cell Deconvolution

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Documentation for package ‘cellGeometry’ version 0.5.4

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

add_noise	Add noise to count data
adjust_library_size	Adjust count matrix by library size
cellMarkers	Identify cell markers
collapse_group	Collapse groups in cellMarkers object
comp_heatmap	Compensation heatmap
cooks.distance.deconv	Regression Deletion Diagnostics
cos_similarity	Gene signature cosine similarity matrix
deconvolute	Deconvolute bulk RNA-Seq using single-cell RNA-Seq signature
diagnose	Diagnostics for cellMarker signatures
fix_bulk	Fix in missing genes in bulk RNA-Seq matrix
gene2symbol	Converts ensembl gene ids to symbols
generate_samples	Generate random cell number samples
gene_angle	Vector based best marker selection
ggplot_residuals	Residuals plot
graded_log_noise	Add noise to count data
log2s	Mean Objects
logmean	Mean Objects
log_noise	Add noise to count data
mergeMarkers	Merge cellMarker signatures
metric_set	Calculate R-squared and metrics on deconvoluted cell subclasses
plot.qqmap	Quantile-quantile plot
plot_comp	Plot compensation analysis
plot_residuals	Residuals plot
plot_set	Scatter plots to compare deconvoluted subclasses
plot_tune	Plot tuning curves
quantile_map	Quantile mapping function between two scRNA-Seq datasets
rank_angle	Rank distance angles from a cosine similarity matrix
reduceNoise	Reduce noise in single-cell data
rstandard.deconv	Regression Deletion Diagnostics
rstudent.deconv	Regression Deletion Diagnostics
scapply	Single-cell apply a function to a matrix split by a factor
scmean	Single-cell mean log gene expression across cell types
shift_noise	Add noise to count data
signature_heatmap	Gene signature heatmap
simulate_bulk	Simulate pseudo-bulk RNA-Seq
slapply	Apply a function to a big matrix by slicing
specificity_plot	Specificity plot
specificity_plotly	Specificity plot
spillover_heatmap	Spillover heatmap
sqrt_noise	Add noise to count data
stack_ggplot	Stacked bar plot
stack_plot	Stacked bar plot
summary.tune_deconv	Summarising deconvolution tuning
trimmean	Mean Objects
tune_deconv	Tune deconvolution parameters
updateMarkers	Update cellMarkers object
violin_plot	Cell subclass violin plot