Package: SEMgraph 1.2.4

Barbara Tarantino

SEMgraph: Network Analysis and Causal Inference Through Structural Equation Modeling

Estimate networks and causal relationships in complex systems through Structural Equation Modeling. This package also includes functions for importing, weight, manipulate, and fit biological network models within the Structural Equation Modeling framework as outlined in the Supplementary Material of Grassi M, Palluzzi F, Tarantino B (2022) <doi:10.1093/bioinformatics/btac567>.

Authors:Mario Grassi [aut], Fernando Palluzzi [aut], Barbara Tarantino [cre]

SEMgraph_1.2.4.tar.gz
SEMgraph_1.2.4.zip(r-4.7-any)SEMgraph_1.2.4.zip(r-4.6-any)SEMgraph_1.2.4.zip(r-4.5-any)
SEMgraph_1.2.4.tgz(r-4.6-any)SEMgraph_1.2.4.tgz(r-4.5-any)
SEMgraph_1.2.4.tar.gz(r-4.7-any)SEMgraph_1.2.4.tar.gz(r-4.6-any)
SEMgraph_1.2.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SEMgraph/json (API)

# Install 'SEMgraph' in R:

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

Bug tracker:https://github.com/fernandopalluzzi/semgraph/issues

Datasets:

alsData - Amyotrophic Lateral Sclerosis (ALS) dataset
kegg - KEGG interactome
kegg.pathways - KEGG pathways
sachs - Sachs multiparameter flow cytometry data and consensus model

On CRAN:

6.37 score 25 stars 1 packages 31 scripts 418 downloads 37 exports 88 dependencies

Last updated from:31eff1eab1. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel	OK	217
source / vignettes	OK	398
linux-release	OK	235
macos-release	OK	236
macos-oldrel	OK	345
windows-devel	OK	156
windows-release	OK	166
windows-oldrel	OK	168
wasm-release	OK	168

Exports:ancestors clusterGraph clusterScore colorGraph cplot dagitty2graph descendants extractClusters factor.analysis gplot graph2dag graph2dagitty graph2lavaan lavaan2graph loadPathways localCI.test mergeNodes modelSearch orientEdges pairwiseMatrix parameterEstimates parents pathFinder properties resizeGraph SEMace SEMbap SEMdag SEMdci SEMgsa SEMpath SEMrun SEMtree Shipley.test siblings transformData weightGraph

Dependencies:AnnotationDbi askpass aspect BH Biobase BiocBaseUtils BiocGenerics BiocManager Biostrings bit bit64 bitops blob boot cachem cherry class cli codetools corpcor cpp11 crayon curl dagitty DBI dir.expiry e1071 fastmap filelock flip foreach gdata generics ggm glasso glmnet glue graph graphite gtools hommel httr igraph IRanges iterators jsonlite KEGGREST lattice lavaan lifecycle lpSolve magrittr MASS Matrix memoise mgcv mime mnormt mvtnorm nlme numDeriv openssl pbapply pbivnorm pkgconfig plyr png protoclust proxy purrr quadprog R6 rappdirs RBGL Rcpp RcppEigen Rgraphviz rlang RSQLite S4Vectors Seqinfo shape someMTP survival sys V8 vctrs XVector

Get started

Rendered fromSEMgraph_tutorial.Rmdusingknitr::rmarkdown

Last update: 2025-12-16
Started: 2025-12-15

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Amyotrophic Lateral Sclerosis (ALS) dataset	alsData
Node ancestry utilities	ancestors ancestry descendants parents siblings
Topological graph clustering	clusterGraph
Module scoring	clusterScore
Vertex and edge graph coloring on the base of fitting	colorGraph
Subgraph mapping	cplot
Graph conversion from dagitty to igraph	dagitty2graph
Cluster extraction utility	extractClusters
Factor analysis for high dimensional data	factor.analysis
Graph plotting with renderGraph	gplot
Convert directed graphs to directed acyclic graphs (DAGs)	graph2dag
Graph conversion from igraph to dagitty	graph2dagitty
Graph to lavaan model	graph2lavaan
KEGG interactome	kegg
KEGG pathways	kegg.pathways
lavaan model to graph	lavaan2graph
Import pathways and generate a reference network	loadPathways
Conditional Independence (CI) local tests of an acyclic graph	localCI.test
Graph nodes merging by a membership attribute	mergeNodes
Optimal model search strategies	modelSearch
Assign edge orientation of an undirected graph	orientEdges
Pairwise plotting of multivariate data	pairwiseMatrix
Parameter Estimates of a fitted SEM	parameterEstimates
Perturbed path search utility	pathFinder
Graph properties summary and graph decomposition	properties
Interactome-assisted graph re-seizing	resizeGraph
Sachs multiparameter flow cytometry data and consensus model	sachs
Compute the Average Causal Effect (ACE) for a given source-sink pair	SEMace
Bow-free covariance search and data de-correlation	SEMbap
Estimate a DAG from an input (or empty) graph	SEMdag
SEM-based differential network analysis	SEMdci
SEM-based gene set analysis	SEMgsa
Search for directed or shortest paths between pairs of source-sink nodes	SEMpath
Fit a graph as a Structural Equation Model (SEM)	SEMrun
Tree-based structure learning methods	SEMtree
Missing edge testing implied by a DAG with Shipley's basis-set	Shipley.test
GGM model summary	summary.GGM
RICF model summary	summary.RICF
Transform data methods	transformData
Graph weighting methods	weightGraph