Package: hcocena 0.99.12

Thomas Ulas

hcocena: Horizontal Integration and Analysis of Multiple Transcriptomics Datasets

Tools for the joint analysis of multiple transcriptomics datasets using a network-based integration approach. The package provides an S4 object model based on MultiAssayExperiment for reproducible analysis of single-layer and multi-layer studies. It includes workflows for clustering, module visualization, functional annotation, upstream inference, and longitudinal follow-up while retaining compatibility helpers for legacy hCoCena objects.

Authors:Thomas Ulas [aut, cre], Waqar Hanif [ctb]

hcocena_0.99.12.tar.gz
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hcocena_0.99.12.tgz(r-4.6-any)hcocena_0.99.12.tgz(r-4.5-any)
hcocena_0.99.12.tar.gz(r-4.7-any)hcocena_0.99.12.tar.gz(r-4.6-any)
hcocena_0.99.12.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
hcocena/json (API)

# Install 'hcocena' in R:

install.packages('hcocena', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/biocompnet/hcocena/issues

On CRAN:

software clustering geneexpression kegg network networkinference transcriptomics workflowstep

3.00 score 110 exports 236 dependencies

Last updated from:d0b918c0e0. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	254
linux-devel	OK	822
source / vignettes	OK	439
linux-release	OK	743
macos-release	OK	676
macos-oldrel	OK	701
windows-devel	OK	643
windows-release	OK	810
windows-oldrel	OK	773
wasm-release	OK	246

Exports:hc_add_meta_time_grouping hc_algo_alluvial hc_antilog hc_auto_set_paths hc_auto_tune hc_auto_tune_cutoff_tiered hc_build_integrated_network hc_celltype_activity_decoupler hc_celltype_annotation hc_change_grouping_parameter hc_check_dirs hc_check_tf hc_cluster_calculation hc_clusters hc_col_anno_categorical hc_col_anno_numerical hc_colour_single_cluster hc_config hc_cut_hclust hc_define_layers hc_example_data hc_export_clusters hc_export_to_cytoscape hc_export_to_local_folder hc_find_hubs hc_functional_enrichment hc_gene_to_cluster hc_get_meta_time_col_order hc_get_module_scores hc_graph hc_highlight_geneset hc_import_clusters hc_import_layout_from_cytoscape hc_import_layout_from_local_folder hc_init hc_init_save_folder hc_integration hc_layer_results hc_list_celltype_databases hc_list_llm_models hc_llm_enrichment hc_llm_import hc_longitudinal_endotype_clustering hc_longitudinal_meta_clustering hc_longitudinal_module_cap hc_longitudinal_module_means hc_longitudinal_step1_module_donor hc_longitudinal_step1_module_donor_direct hc_longitudinal_step2_meta_clustering hc_longitudinal_step3_meta_module_trajectories hc_longitudinal_workflow_direct hc_mae hc_merge_clusters hc_meta_correlation_cat hc_meta_correlation_num hc_meta_plot hc_module_condition_significance hc_module_gfc_tables hc_network_comparison_1 hc_network_comparison_2 hc_pca hc_pca_algo_compare hc_plot_celltype_annotation_matrix hc_plot_cluster_heatmap hc_plot_cluster_heatmap_view hc_plot_cutoffs hc_plot_deg_dist hc_plot_enrichment_panels hc_plot_enrichment_upstream_network hc_plot_gfc_network hc_plot_integrated_network hc_plot_llm_enrichment hc_plot_longitudinal_cap hc_plot_longitudinal_endotype_meta_flow hc_plot_longitudinal_endotypes hc_plot_longitudinal_enrichment_meta_waves hc_plot_longitudinal_enrichment_waves hc_plot_longitudinal_k_criterion hc_plot_longitudinal_meta_consensus hc_plot_longitudinal_meta_embeddings hc_plot_longitudinal_meta_module_waves hc_plot_longitudinal_module_clusters hc_plot_longitudinal_module_means hc_plot_sample_distributions hc_preview_celltype_database hc_print_longitudinal_endotypes hc_read_data hc_read_supplementary hc_regroup_samples hc_resolve_paths hc_run_expression_analysis_1 hc_run_expression_analysis_2 hc_satellite hc_set_cutoff hc_set_global_settings hc_set_layer_settings hc_set_paths hc_set_supp_files hc_split_modules hc_suggest_topvar hc_tf_overrep_module hc_tf_overrep_network hc_tune_cutoff hc_tune_resolution hc_unsplit_modules hc_update_clustering_algorithm hc_upstream_inference hc_user_specific_cluster_profiling hc_visualize_gene_expression hc_write_session_info

Dependencies:abind aisdk AnnotationDbi ape aplot askpass backports base64enc BH Biobase BiocBaseUtils BiocGenerics Biostrings bit bit64 blob boot broom bslib cachem Cairo callr car carData checkmate circlize cli clipr clue cluster clusterProfiler codetools colorspace ComplexHeatmap corrplot cowplot cpp11 crayon crosstalk curl data.table DBI DelayedArray dendextend Deriv digest doBy doParallel DOSE dplyr dqrng DT ellipse emmeans enrichit enrichplot estimability evaluate factoextra FactoMineR farver fastmap flashClust FNN fontawesome fontBitstreamVera fontLiberation fontquiver foreach forecast foreign Formula fracdiff fs gdtools generics GenomicRanges GetoptLong ggforce ggfun ggiraph ggnewscale ggplot2 ggplotify ggpubr ggrepel ggsci ggsignif ggtangle ggtree GlobalOptions glue GO.db GOSemSim gridExtra gridGraphics gson gtable gtools highr Hmisc hms htmlTable htmltools htmlwidgets httr httr2 igraph IRanges irlba isoband iterators jquerylib jsonlite KEGGREST knitr labeling later lattice lazyeval leaps leidenAlg leidenbase lifecycle lme4 lmtest magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats memoise mgcv mime minqa modelr multcompView MultiAssayExperiment mvtnorm nlme nloptr nnet numDeriv openssl openxlsx otel patchwork pbkrtest pbmcapply pheatmap pillar pkgconfig plotly plyr png polyclip polynom prettyunits pROC processx progress promises ps purrr quantreg qvalue R6 rappdirs rbibutils RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppProgress Rdpack readr reformulas reshape2 rjson rlang rlist rmarkdown rpart RSpectra RSQLite rstatix rstudioapi S4Arrays S4Vectors S7 sass scales scatterpie scatterplot3d sccore Seqinfo shape showtext showtextdb sitmo SparseArray SparseM stringi stringr SummarizedExperiment survival sys sysfonts systemfonts tibble tidydr tidyr tidyselect tidytree timeDate tinytex treeio tweenr tzdb urca utf8 uwot vctrs viridis viridisLite vroom withr xfun XML XVector yaml yulab.utils zip zoo

hcocena: a complete worked analysis

Rendered fromhcocena-s4-workflow.Rmdusingknitr::rmarkdown

Last update: 2026-10-03
Started: 2026-09-25

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Add meta-cluster x time grouping column for heatmap regrouping	hc_add_meta_time_grouping
algo alluvial	hc_algo_alluvial
Reverse a log transformation	hc_antilog
Resolve and apply standard paths in one call	hc_auto_set_paths
Automatically tune key hCoCena parameters	hc_auto_tune
Tiered and robust cutoff recommendation	hc_auto_tune_cutoff_tiered
Network integration	hc_build_integrated_network
Module cell-type activity from Enrichr markers via decoupleR (S4 API)	hc_celltype_activity_decoupler
Module cell-type annotation from Enrichr (S4 API)	hc_celltype_annotation
change grouping parameter	hc_change_grouping_parameter
Fixes Directories	hc_check_dirs
Check TF targets (S4 API)	hc_check_tf
Cluster Calculation	hc_cluster_calculation
Access cluster information from an 'HCoCenaExperiment'	hc_clusters hc_clusters,HCoCenaExperiment-method
Add categorical module heatmap annotations (S4 API)	hc_col_anno_categorical
Add numeric module heatmap annotations (S4 API)	hc_col_anno_numerical
Highlight single cluster in network (S4 API)	hc_colour_single_cluster
Access configuration from an 'HCoCenaExperiment'	hc_config hc_config,HCoCenaExperiment-method
Cut a hierarchical clustering tree to regroup samples (S4 API)	hc_cut_hclust
Define layers in an 'HCoCenaExperiment'	hc_define_layers
Load an example 'HCoCenaExperiment'	hc_example_data
export clusters	hc_export_clusters
Export network to Cytoscape (S4 API)	hc_export_to_cytoscape
Export network to local folder (S4 API)	hc_export_to_local_folder
Hub detection (S4 API)	hc_find_hubs
Functional enrichment (S4 API)	hc_functional_enrichment
Gene-to-module table (S4 API)	hc_gene_to_cluster
Get column order for meta-cluster x timepoint heatmaps	hc_get_meta_time_col_order
get module scores	hc_get_module_scores
Access the integrated network of an 'HCoCenaExperiment'	hc_graph hc_graph,HCoCenaExperiment-method
Highlight gene set in network (S4 API)	hc_highlight_geneset
Import an external gene-to-cluster assignment	hc_import_clusters
Import layout from Cytoscape (S4 API)	hc_import_layout_from_cytoscape
Import Cytoscape layout from local folder (S4 API)	hc_import_layout_from_local_folder
Initialize an empty 'HCoCenaExperiment'	hc_init
Creates a Save Folder	hc_init_save_folder
Access integration payload from an 'HCoCenaExperiment'	hc_integration hc_integration,HCoCenaExperiment-method
Access layer results from an 'HCoCenaExperiment'	hc_layer_results hc_layer_results,HCoCenaExperiment-method
List Enrichr cell-type related databases	hc_list_celltype_databases
List Available LLM Models	hc_list_llm_models
LLM-based interpretation of modules or feature sets	hc_llm_enrichment
Import an answer from a provider's web chat	hc_llm_import
Cluster donors into longitudinal endotypes	hc_longitudinal_endotype_clustering
Meta-cluster donors based on longitudinal CAP features	hc_longitudinal_meta_clustering
Compute module-level CAP matrix from repeated trajectory clustering	hc_longitudinal_module_cap
Build longitudinal module means per donor and timepoint	hc_longitudinal_module_means
Longitudinal step 1: module/donor clustering	hc_longitudinal_step1_module_donor
Longitudinal step 1: module/donor clustering with direct trajectories	hc_longitudinal_step1_module_donor_direct
Longitudinal step 2: meta-clustering	hc_longitudinal_step2_meta_clustering
Longitudinal step 3: module trajectories by meta-cluster	hc_longitudinal_step3_meta_module_trajectories
Convenience longitudinal workflow using the direct step-1 backend	hc_longitudinal_workflow_direct
Access 'MultiAssayExperiment' from an 'HCoCenaExperiment'	hc_mae hc_mae,HCoCenaExperiment-method
Merge similar modules	hc_merge_clusters
Correlate categorical metadata with modules (S4 API)	hc_meta_correlation_cat
Correlate numeric metadata with modules (S4 API)	hc_meta_correlation_num
meta plot	hc_meta_plot
Test module differences between conditions (S4 API)	hc_module_condition_significance
Module GFC per group and per sample	hc_module_gfc_tables
Compare two gene-to-cluster assignments	hc_network_comparison_1
Compare the edges of two networks for a set of genes	hc_network_comparison_2
pca	hc_pca
pca algo compare	hc_pca_algo_compare
Plot module x cell-type matrix from module cell-type annotation	hc_plot_celltype_annotation_matrix
Plot module heatmap (S4 API)	hc_plot_cluster_heatmap
Plot a fixed-scale view of selected modules from the module heatmap	hc_plot_cluster_heatmap_view
plot cutoffs	hc_plot_cutoffs
Plot degree distributions (S4 API)	hc_plot_deg_dist
Draw saved functional-enrichment panels from the current object	hc_plot_enrichment_panels
Plot module knowledge network from enrichment + upstream inference (S4 API)	hc_plot_enrichment_upstream_network
plot gfc network	hc_plot_gfc_network
Plot integrated network (S4 API)	hc_plot_integrated_network
Plot LLM-based module interpretations	hc_plot_llm_enrichment
Plot CAP heatmap (donor x module-cluster proportions)	hc_plot_longitudinal_cap
Plot endotype-to-meta-cluster flow as Sankey diagram	hc_plot_longitudinal_endotype_meta_flow
Plot longitudinal endotype results	hc_plot_longitudinal_endotypes
Plot longitudinal enrichment waves by meta-cluster	hc_plot_longitudinal_enrichment_meta_waves
Plot longitudinal enrichment waves for top terms per module	hc_plot_longitudinal_enrichment_waves
Plot k-criterion diagnostics for longitudinal clustering	hc_plot_longitudinal_k_criterion
Plot consensus diagnostics for longitudinal meta-clustering	hc_plot_longitudinal_meta_consensus
Plot meta-clustering embeddings and endotype cross-tab	hc_plot_longitudinal_meta_embeddings
Plot module trajectories by donor meta-cluster	hc_plot_longitudinal_meta_module_waves
Plot module-wise trajectory clusters and cluster heatmap	hc_plot_longitudinal_module_clusters
Plot donor-level module trajectories (faint donors + mean line)	hc_plot_longitudinal_module_means
plot sample distributions	hc_plot_sample_distributions
Preview terms and genes from one Enrichr database	hc_preview_celltype_database
Print longitudinal endotype outputs	hc_print_longitudinal_endotypes
Function To Read All Count And Annotation Files	hc_read_data
Read Supplementary Data	hc_read_supplementary
Regroup samples from module-level fold-change profiles	hc_regroup_samples
Resolve hCoCena input/output directories for Docker or local projects	hc_resolve_paths
Run First Part Of The Gene Expression Analysis	hc_run_expression_analysis_1
Run Second Part Of The Gene Expression Analysis	hc_run_expression_analysis_2
Access downstream results stored in an 'HCoCenaExperiment'	hc_satellite hc_satellite,HCoCenaExperiment-method
Set network cutoffs (S4 API)	hc_set_cutoff
Define Global Settings	hc_set_global_settings
Define Layer Settings	hc_set_layer_settings
Set input/output paths in an 'HCoCenaExperiment'	hc_set_paths
Set Supplementary Files	hc_set_supp_files
Split one or multiple modules into submodules (S4 API)	hc_split_modules
suggest topvar	hc_suggest_topvar
TF enrichment per module (S4 API)	hc_tf_overrep_module
TF enrichment network-wide (S4 API)	hc_tf_overrep_network
Robust tiered correlation-cutoff tuning	hc_tune_cutoff
Tune clustering algorithm and resolution	hc_tune_resolution
Undo module splitting (S4 API)	hc_unsplit_modules
update clustering algorithm	hc_update_clustering_algorithm
Upstream regulator/pathway inference (S4 API)	hc_upstream_inference
Profile modules against user-defined enrichment terms	hc_user_specific_cluster_profiling
Visualize gene expression (S4 API)	hc_visualize_gene_expression
write session info	hc_write_session_info
hCoCena S4 Classes	HCoCenaClasses HCoCenaConfig-class HCoCenaExperiment-class HCoCenaIntegration-class HCoCenaLayerResult-class HCoCenaReferences-class
Plot sample-regrouping heatmaps	plot.hc_sample_regrouping