Package: SEMgraph 1.2.2

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 to import, weight, manipulate, and fit biological network models within the Structural Equation Modeling framework proposed in Grassi M, Palluzzi F, Tarantino B (2022) <doi:10.1093/bioinformatics/btac567>.

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

SEMgraph_1.2.2.tar.gz
SEMgraph_1.2.2.tar.gz(r-4.5-noble)SEMgraph_1.2.2.tar.gz(r-4.4-noble)
SEMgraph_1.2.2.tgz(r-4.4-emscripten)SEMgraph_1.2.2.tgz(r-4.3-emscripten)
SEMgraph.pdf |SEMgraph.html✨
SEMgraph/json (API)
NEWS

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

Peer review:

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

36 exports 4 stars 0.82 score 57 dependencies 19 scripts 437 downloads

Last updated 2 months agofrom:79650b1ef7. Checks:OK: 2. Indexed: no.

TargetResultDate
Doc / VignettesOKAug 22 2024
R-4.5-linuxOKAug 22 2024

Exports:ancestorsclusterGraphclusterScorecolorGraphcplotdagitty2graphdescendantsextractClustersfactor.analysisgplotgraph2daggraph2dagittygraph2lavaanlavaan2graphlocalCI.testmergeNodesmodelSearchorientEdgespairwiseMatrixparameterEstimatesparentspathFinderpropertiesresizeGraphSEMaceSEMbapSEMdagSEMdciSEMgsaSEMpathSEMrunSEMtreeShipley.testsiblingstransformDataweightGraph

Dependencies:aspectBHBiocGenericsBiocManagerbitopsbootcherryclassclicodetoolscorpcorcpp11curldagittye1071flipforeachgdataggmglassoglmnetgluegraphgtoolshommeligraphiteratorsjsonlitelatticelavaanlifecyclelpSolvemagrittrMASSMatrixmgcvmnormtmvtnormnlmenumDerivpbapplypbivnormpkgconfigplyrprotoclustproxyquadprogRBGLRcppRcppEigenRgraphvizrlangshapesomeMTPsurvivalV8vctrs

Readme and manuals

Help Manual

Help pageTopics
Amyotrophic Lateral Sclerosis (ALS) datasetalsData
Node ancestry utilitiesancestors ancestry descendants parents siblings
Topological graph clusteringclusterGraph
Module scoringclusterScore
Vertex and edge graph coloring on the base of fittingcolorGraph
Subgraph mappingcplot
Graph conversion from dagitty to igraphdagitty2graph
Cluster extraction utilityextractClusters
Factor analysis for high dimensional datafactor.analysis
Graph plotting with renderGraphgplot
Convert directed graphs to directed acyclic graphs (DAGs)graph2dag
Graph conversion from igraph to dagittygraph2dagitty
Graph to lavaan modelgraph2lavaan
KEGG interactomekegg
KEGG pathwayskegg.pathways
lavaan model to graphlavaan2graph
Conditional Independence (CI) local tests of an acyclic graphlocalCI.test
Graph nodes merging by a membership attributemergeNodes
Optimal model search strategiesmodelSearch
Assign edge orientation of an undirected graphorientEdges
Pairwise plotting of multivariate datapairwiseMatrix
Parameter Estimates of a fitted SEMparameterEstimates
Perturbed path search utilitypathFinder
Graph properties summary and graph decompositionproperties
Interactome-assisted graph re-seizingresizeGraph
Sachs multiparameter flow cytometry data and consensus modelsachs
Compute the Average Causal Effect (ACE) for a given source-sink pairSEMace
Bow-free covariance search and data de-correlationSEMbap
Estimate a DAG from an input (or empty) graphSEMdag
SEM-based differential network analysisSEMdci
SEM-based gene set analysisSEMgsa
Search for directed or shortest paths between pairs of source-sink nodesSEMpath
Fit a graph as a Structural Equation Model (SEM)SEMrun
Tree-based structure learning methodsSEMtree
Missing edge testing implied by a DAG with Shipley's basis-setShipley.test
GGM model summarysummary.GGM
RICF model summarysummary.RICF
Transform data methodstransformData
Graph weighting methodsweightGraph