Package: FastCCCR 1.0.0

FastCCCR: Fast Cell-Cell Communication Analysis with Statistical Framework

A high-performance R package for cell-cell communication (CCC) analysis in single-cell RNA sequencing data. FastCCCR implements an innovative statistical framework based on exact null distribution computation, Cauchy combination of multiple statistical methods, and reference-based inference. The package is optimized with Rcpp for computational efficiency and supports both Seurat V4 and V5 objects. Key features include: (1) Multiple scoring methods with Cauchy combination, (2) Reference panel construction and query inference, (3) Support for multiple ligand-receptor databases (CellPhoneDB, CellChat, NicheNet), (4) High-performance vectorized and parallel computation.

Authors:Zaoqu Liu [aut, cre], Wenjing Zhong [ctb], Marvin Yao [ctb]

FastCCCR_1.0.0.tar.gz
FastCCCR_1.0.0.zip(r-4.7)FastCCCR_1.0.0.zip(r-4.6)FastCCCR_1.0.0.zip(r-4.5)
FastCCCR_1.0.0.tgz(r-4.6-x86_64)FastCCCR_1.0.0.tgz(r-4.6-arm64)FastCCCR_1.0.0.tgz(r-4.5-x86_64)FastCCCR_1.0.0.tgz(r-4.5-arm64)
FastCCCR_1.0.0.tar.gz(r-4.7-arm64)FastCCCR_1.0.0.tar.gz(r-4.7-x86_64)FastCCCR_1.0.0.tar.gz(r-4.6-arm64)FastCCCR_1.0.0.tar.gz(r-4.6-x86_64)
FastCCCR_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
FastCCCR/json (API)

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

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

Pkgdown/docs site:https://zaoqu-liu.github.io

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

Conda:

cpp

2.48 score 3 stars 6 scripts 52 exports 16 dependencies

Last updated from:e2454107b9 (on main). Checks:12 ERROR, 1 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64ERROR203
linux-devel-x86_64ERROR206
source / vignettesERROR254
linux-release-arm64ERROR195
linux-release-x86_64ERROR195
macos-release-arm64ERROR124
macos-release-x86_64ERROR254
macos-oldrel-arm64ERROR105
macos-oldrel-x86_64ERROR232
windows-develERROR167
windows-releaseERROR225
windows-oldrelERROR220
wasm-releaseOK168

Exports:analyze_interactions_percentsbatch_compute_gene_distributions_cppbatch_compute_pvalues_cppbuild_referencecalculate_cluster_meancalculate_cluster_mean_distributioncalculate_cluster_means_cppcalculate_cluster_percentscalculate_cluster_percents_cppcalculate_cluster_quantilecalculate_cluster_quantile_distributioncalculate_cluster_quantiles_cppcalculate_interaction_strengths_cppcalculate_interactions_pvaluecalculate_interactions_strengthcauchy_combinecauchy_combine_cppcauchy_combine_filescauchy_combine_with_statcheck_interactions_by_DEGcluster_markers_methodcombine_complex_distributioncombine_complex_distribution_dtcreate_distributioncreate_significant_dfdigitize_transform_cppDistributionfast_histogram_cppfastcccfastccc_cauchyfft_convolve_cppget_average_distributionget_count_dataget_input_dataget_input_data_from_filesget_interactionsget_minimum_distributionget_minimum_distribution_cppget_network_dataget_pmf_from_digit_samplesget_pvalueget_pvalues_from_pmf_cppget_strength_network_dataget_thresholdinfer_queryload_reference_configmultiply_distributions_cppplot_ccc_chordplot_ccc_heatmapplot_ccc_networkstatistical_analysis_methodsum_distributions_cpp

Dependencies:clicodetoolsdata.tabledigestfuturefuture.applyglobalslatticelistenvMatrixparallellyprogressrR6RcppRcppArmadillorlang

Readme and manuals

Help Manual

Help pageTopics
FastCCCR: Fast Cell-Cell Communication AnalysisFastCCCR-package FastCCCR
Analyze Interaction Percentagesanalyze_interactions_percents
Batch compute gene sum distributionsbatch_compute_gene_distributions_cpp
Batch compute p-values for L-R interactionsbatch_compute_pvalues_cpp
Build Reference Panelbuild_reference
Reference Building Functionsbuild-reference
Calculate Cluster Mean Expressioncalculate_cluster_mean
Calculate Cluster Mean Distributioncalculate_cluster_mean_distribution
Calculate cluster means (vectorized)calculate_cluster_means_cpp
Calculate Cluster Expression Percentagescalculate_cluster_percents
Calculate cluster expression percentagescalculate_cluster_percents_cpp
Calculate Cluster Quantile Expressioncalculate_cluster_quantile
Calculate Cluster Quantile Distributioncalculate_cluster_quantile_distribution
Calculate cluster quantiles (vectorized)calculate_cluster_quantiles_cpp
Calculate interaction strengths (vectorized)calculate_interaction_strengths_cpp
Calculate Interaction P-valuescalculate_interactions_pvalue
Calculate Interaction Strengthscalculate_interactions_strength
Cauchy Combination of P-valuescauchy_combine
Cauchy combination of p-valuescauchy_combine_cpp
Cauchy Combine from Filescauchy_combine_files
Cauchy Combine with Statisticcauchy_combine_with_stat
Cauchy Combination Functionscauchy-combine
Check Interactions by DEGcheck_interactions_by_DEG
Cluster Markers Methodcluster_markers_method
Combine Complex Distributioncombine_complex_distribution
Combine Complex Distributioncombine_complex_distribution_dt
Core Functions for FastCCCRcore
Create Distribution from Samplescreate_distribution
Create Significant Interactions DataFramecreate_significant_df
Data Preprocessing Functions for FastCCCRdata-preprocess
Digitize transform for rank-based analysisdigitize_transform_cpp
Complex Distribution Functionsdist-complex
IID Set Distribution Functionsdist-iid-set
L-R Distribution and P-value Functionsdist-lr
Distribution Class for FastCCCRDistribution
Fast histogram for PMF computationfast_histogram_cpp
Simplified FastCCC Functionfastccc
FastCCC with Cauchy Combinationfastccc_cauchy
FFT Convolutionfft_convolve_cpp
Get Average Distributionget_average_distribution
Get Count Data Onlyget_count_data
Get Input Data from Seurat Objectget_input_data
Load Data from Filesget_input_data_from_files
Get Interactions from Databaseget_interactions
Get Minimum Distributionget_minimum_distribution
Minimum Distributionget_minimum_distribution_cpp
Get Network Dataget_network_data
Get PMF Array from Digitized Samplesget_pmf_from_digit_samples
Get p-value from Distributionget_pvalue
Calculate P-values from PMF (vectorized)get_pvalues_from_pmf_cpp
Get Strength Network Dataget_strength_network_data
Get threshold from Distribution (for significance)get_threshold
Infer Query Using Referenceinfer_query
Query Inference Functionsinfer-query
Load Reference Configload_reference_config
Multiply Distributionsmultiply_distributions_cpp
Plot CCC Chord Diagramplot_ccc_chord
Plot CCC Heatmapplot_ccc_heatmap
Plot CCC Networkplot_ccc_network
Score Calculation Functions for FastCCCRscore
FastCCC Single Methodstatistical_analysis_method
Sum Distributions (for average)sum_distributions_cpp
Visualization Functions for FastCCCRvisualize