This package is considered a duplicate. The official version of this package is found at:https://myles-lewis.r-universe.dev/cellGeometry

Package: cellGeometry 0.5.8

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.

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

cellGeometry_0.5.8.tar.gz
cellGeometry_0.5.8.zip(r-4.7)cellGeometry_0.5.8.zip(r-4.6)cellGeometry_0.5.8.zip(r-4.5)
cellGeometry_0.5.8.tgz(r-4.6-any)cellGeometry_0.5.8.tgz(r-4.5-any)
cellGeometry_0.5.8.tar.gz(r-4.7-any)cellGeometry_0.5.8.tar.gz(r-4.6-any)
cellGeometry_0.5.8.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://zaoqu-liu.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/zaoqu-liu/cellgeometry/issues

On CRAN:

2.38 score 48 scripts 538 downloads 41 exports 106 dependencies

Last updated from:bfc1786417 (on main). Checks:7 WARNING, 1 ERROR, 1 OK. Indexed: no.

Target	Result	Time
linux-devel-x86_64	WARNING	391
source / vignettes	ERROR	334
linux-release-x86_64	WARNING	372
macos-release-arm64	WARNING	294
macos-oldrel-arm64	WARNING	365
windows-devel	WARNING	334
windows-release	WARNING	302
windows-oldrel	WARNING	289
wasm-release	OK	174

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 mergeMarkers metric_set plot_comp plot_residuals plot_set plot_tune quantile_map rank_angle reduceNoise scapply scmean 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 pbmcapply 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

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

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
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
Mean Objects	log2s logmean trimmean
Merge cellMarker signatures	mergeMarkers
Calculate R-squared and metrics on deconvoluted cell subclasses	metric_set
Plot compensation analysis	plot_comp
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
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