Package: SimiCviz 0.99.2

Irene Marín-Goñi

SimiCviz: Visualization Tools for Gene Regulatory Network Analysis

Visualization and export utilities for SimiC and SimiCPipeline outputs. The package focuses on importing SimiC-style results (e.g., weights, AUC metrics) from pickle/CSV files, processing and generating publication-ready plots (networks, heatmaps, distributions) and tables saved into a reproducible, ordered directory hierarchy.

Authors:Irene Marín-Goñi [aut, cre]

SimiCviz_0.99.2.tar.gz
SimiCviz_0.99.2.zip(r-4.7-any)SimiCviz_0.99.2.zip(r-4.6-any)SimiCviz_0.99.2.zip(r-4.5-any)
SimiCviz_0.99.2.tgz(r-4.6-any)SimiCviz_0.99.2.tgz(r-4.5-any)
SimiCviz_0.99.2.tar.gz(r-4.7-any)SimiCviz_0.99.2.tar.gz(r-4.6-any)
SimiCviz_0.99.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SimiCviz/json (API)

# Install 'SimiCviz' in R:

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

Bug tracker:https://github.com/ml4bm-lab/simicviz/issues

On BioConductor:SimiCviz-0.99.2(bioc 3.24)

software visualization generegulation networkinference network singlecell

4.60 score 1 stars 6 scripts 652 downloads 33 exports 65 dependencies

Last updated from:ba290d224a. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	153
linux-devel	OK	232
source / vignettes	OK	254
linux-release	OK	215
macos-release	OK	164
macos-oldrel	OK	166
windows-devel	OK	216
windows-release	OK	172
windows-oldrel	OK	181
wasm-release	OK	140

Exports:auc_list_to_df AUCProcessor calculate_activity_scores calculate_dissimilarity calculate_ecdf_auc compute_auc export_SimiCviz_csv get_auc get_tf_network is.SimiCvizExperiment load_cell_labels load_collected_auc load_expression_matrix load_from_csv load_SimiCPipeline plot_auc_cumulative plot_auc_distributions plot_auc_heatmap plot_auc_summary_statistics plot_dissimilarity_heatmap plot_r2_distribution plot_target_weights plot_tf_network_heatmap plot_tf_weights read_auc_csv read_auc_pickle read_pickle read_weights_csv read_weights_pickle setCellLabels setLabelNames show SimiCvizExperiment

Dependencies:abind BH Biobase BiocGenerics BiocParallel cli codetools colorspace cpp11 DelayedArray dplyr farver formatR futile.logger futile.options generics GenomicRanges ggplot2 glue gridExtra gtable here IRanges isoband jsonlite labeling lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats pillar pkgconfig plyr png purrr R6 rappdirs RColorBrewer Rcpp RcppTOML reshape2 reticulate rlang rprojroot S4Arrays S4Vectors S7 scales Seqinfo snow SparseArray stringi stringr SummarizedExperiment tibble tidyr tidyselect utf8 vctrs viridisLite withr XVector

SimiCviz: Visualization and Analysis of Gene Regulatory Networks

Rendered fromSimiCviz.Rmdusingknitr::rmarkdown

Last update: 2026-07-04
Started: 2026-03-09

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Compute AUC for a single cell	.compute_cell_auc
Validate expression matrix is in genes x cells format	.ensure_genes_x_cells_format
Collect per-label AUC matrices using cell labels	auc_list_to_df
Initialize AUCProcessor	AUCProcessor
AUCProcessor class	AUCProcessor-class show,AUCProcessor-method
Calculate activity scores from SimiCvizExperiment weights	calculate_activity_scores
Calculate dissimilarity scores across phenotype labels	calculate_dissimilarity
Calculate ECDF AUC	calculate_ecdf_auc
Compute activity scores for an object	compute_auc
Compute activity scores for all cells	compute_auc,AUCProcessor-method
Export SimiCvizExperiment tables to CSV	export_SimiCviz_csv
Extract activity scores from an object	get_auc
Get computed activity scores	get_auc,AUCProcessor-method
Extract stacked TF-target weight matrix across labels	get_tf_network
Check if object is a SimiCvizExperiment	is.SimiCvizExperiment
Load cell-to-label mapping	load_cell_labels
Load a collected AUC CSV into a data.frame	load_collected_auc
Load expression matrix from various sources /file formats Allowed formats: • CSV file • h5ad file • rds file (Seurat or SingleCellExperiment object) • matrix or data.frame in R	load_expression_matrix
Create a SimiCvizExperiment from CSV files	load_from_csv
Create a SimiCvizExperiment from SimiCPipeline output path	load_SimiCPipeline
Plot AUC cumulative (ECDF) curves by label	plot_auc_cumulative
Plot AUC density distributions by label	plot_auc_distributions
Plot mean AUC heatmap by TF and label	plot_auc_heatmap
Plot AUC summary statistics	plot_auc_summary_statistics
Plot dissimilarity heatmap	plot_dissimilarity_heatmap
Plot adjusted R² distributions	plot_r2_distribution
Plot weight barplots for target genes	plot_target_weights
Plot heatmap of a TF regulatory network across phenotypes	plot_tf_network_heatmap
Plot weight barplots for transcription factors	plot_tf_weights
Read SimiC-style AUC results from CSV (compatibility)	read_auc_csv
Read SimiCPipeline output AUC matrices (pickle file)	read_auc_pickle
Read pickle files	read_pickle
Read Long-style TF-target weights from CSV (compatibility)	read_weights_csv
Read SimiCPipeline output weights (pickle file)	read_weights_pickle
Set or update cell-to-label mapping	setCellLabels
Set or update label names and colors	setLabelNames
Construct a SimiCvizExperiment object	SimiCvizExperiment
SimiCvizExperiment class	show,SimiCvizExperiment-method SimiCvizExperiment-class