Package: SimiCviz 0.99.0

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_0.99.0.tar.gz
SimiCviz_0.99.0.zip(r-4.7)SimiCviz_0.99.0.zip(r-4.6)SimiCviz_0.99.0.zip(r-4.5)
SimiCviz_0.99.0.tgz(r-4.6-any)SimiCviz_0.99.0.tgz(r-4.5-any)
SimiCviz_0.99.0.tar.gz(r-4.7-any)SimiCviz_0.99.0.tar.gz(r-4.6-any)
SimiCviz_0.99.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
SimiCviz/json (API)
NEWS

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

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

On CRAN:

Conda:

softwarevisualizationgeneregulationnetworkinferencenetworksinglecell

3.54 score 1 stars 4 scripts 33 exports 65 dependencies

Last updated from:55d1dd2705. Checks:1 NOTE, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE166
linux-devel-x86_64OK201
source / vignettesOK299
linux-release-x86_64OK193
macos-release-arm64OK109
macos-oldrel-arm64OK138
windows-develOK221
windows-releaseOK302
windows-oldrelOK192
wasm-releaseOK157

Exports:auc_list_to_dfAUCProcessorcalculate_activity_scorescalculate_dissimilaritycalculate_ecdf_auccompute_aucexport_SimiCviz_csvget_aucget_tf_networkis.SimiCvizExperimentload_cell_labelsload_collected_aucload_expression_matrixload_from_csvload_SimiCPipelineplot_auc_cumulativeplot_auc_distributionsplot_auc_heatmapplot_auc_summary_statisticsplot_dissimilarity_heatmapplot_r2_distributionplot_target_weightsplot_tf_network_heatmapplot_tf_weightsread_auc_csvread_auc_pickleread_pickleread_weights_csvread_weights_picklesetCellLabelssetLabelNamesshowSimiCvizExperiment

Dependencies:abindBHBiobaseBiocGenericsBiocParallelclicodetoolscolorspacecpp11DelayedArraydplyrfarverformatRfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegridExtragtablehereIRangesisobandjsonlitelabelinglambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatspillarpkgconfigplyrpngpurrrR6rappdirsRColorBrewerRcppRcppTOMLreshape2reticulaterlangrprojrootS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraystringistringrSummarizedExperimenttibbletidyrtidyselectutf8vctrsviridisLitewithrXVector

SimiCviz: Visualization and Analysis of Gene Regulatory Networks

Irene Marín-Goñi

Rendered fromSimiCviz.Rmdusingknitr::rmarkdownon Jun 08 2026.

Last update: 2026-05-01
Started: 2026-03-09

Readme and manuals

Help Manual

Help pageTopics
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 labelsauc_list_to_df
Initialize AUCProcessorAUCProcessor
AUCProcessor classAUCProcessor-class show,AUCProcessor-method
Calculate activity scores from SimiCvizExperiment weightscalculate_activity_scores
Calculate dissimilarity scores across phenotype labelscalculate_dissimilarity
Calculate ECDF AUCcalculate_ecdf_auc
Compute activity scores for an objectcompute_auc
Compute activity scores for all cellscompute_auc,AUCProcessor-method
Export SimiCvizExperiment tables to CSVexport_SimiCviz_csv
Extract activity scores from an objectget_auc
Get computed activity scoresget_auc,AUCProcessor-method
Extract stacked TF-target weight matrix across labelsget_tf_network
Check if object is a SimiCvizExperimentis.SimiCvizExperiment
Load cell-to-label mappingload_cell_labels
Load a collected AUC CSV into a data.frameload_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 Rload_expression_matrix
Create a SimiCvizExperiment from CSV filesload_from_csv
Create a SimiCvizExperiment from SimiCPipeline output pathload_SimiCPipeline
Plot AUC cumulative (ECDF) curves by labelplot_auc_cumulative
Plot AUC density distributions by labelplot_auc_distributions
Plot mean AUC heatmap by TF and labelplot_auc_heatmap
Plot AUC summary statisticsplot_auc_summary_statistics
Plot dissimilarity heatmapplot_dissimilarity_heatmap
Plot adjusted R² distributionsplot_r2_distribution
Plot weight barplots for target genesplot_target_weights
Plot heatmap of a TF regulatory network across phenotypesplot_tf_network_heatmap
Plot weight barplots for transcription factorsplot_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 filesread_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 mappingsetCellLabels
Set or update label names and colorssetLabelNames
Construct a SimiCvizExperiment objectSimiCvizExperiment
SimiCvizExperiment classshow,SimiCvizExperiment-method SimiCvizExperiment-class