Package: genewalkR 0.2.3

genewalkR: Graph-based computational algorithms in R, including diffusions and small neural networks like node2vec.

Various graph-based methods commonly used in computational biology. Heat diffusions over networks, node2vec and metapath2vec-based analyses over biologicals networks in R powered by Rust. Includes GeneWalkR and co-expression gene drift detection methods based on node2vec.

Authors:Gregor Lueg [aut, cre], Mi Trinh [ctb]

genewalkR_0.2.3.tar.gz
genewalkR_0.2.3.zip(r-4.7-x86_64)genewalkR_0.2.3.zip(r-4.7-arm64)genewalkR_0.2.3.zip(r-4.6-x86_64)genewalkR_0.2.3.zip(r-4.6-arm64)genewalkR_0.2.3.zip(r-4.5-x86_64)
genewalkR_0.2.3.tgz(r-4.6-x86_64)genewalkR_0.2.3.tgz(r-4.6-arm64)genewalkR_0.2.3.tgz(r-4.5-x86_64)genewalkR_0.2.3.tgz(r-4.5-arm64)
genewalkR_0.2.3.tar.gz(r-4.7-arm64)genewalkR_0.2.3.tar.gz(r-4.7-x86_64)genewalkR_0.2.3.tar.gz(r-4.6-arm64)genewalkR_0.2.3.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
genewalkR/json (API)

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

Bug tracker:https://github.com/gregorlueg/genewalkr/issues

Pkgdown/docs site:https://gregorlueg.github.io

Datasets:

On CRAN:

Conda:

bioinformaticscomputational-biologydeep-learningnetwork-analysisnode2vecrustcargoquarto

5.12 score 2 stars 7 scripts 75 exports 81 dependencies

Last updated from:78a366b0f2 (on main). Checks:13 NOTE, 1 OK, 1 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
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linux-devel-x86_64NOTE357
source / vignettesOK750
linux-release-arm64NOTE262
linux-release-x86_64NOTE294
macos-release-arm64NOTE356
macos-release-x86_64NOTE958
macos-oldrel-arm64NOTE428
macos-oldrel-x86_64NOTE940
windows-devel-arm64NOTE598
windows-devel-x86_64NOTE569
windows-release-arm64NOTE767
windows-release-x86_64NOTE348
windows-oldrel-x86_64NOTE339
wasm-releaseFAIL156

Exports:build_kernelcalculate_driftcalculate_genewalk_statscalculate_profile_distancescheck_degree_distributiondedup_edgesdifferential_graph_test_datadiffuse_scoresdiffusion_test_latticeDiffusionProfilesDiffusionScoresdownload_databaseEmbedDriftevaluate_node2vec_testgenerate_initial_embgenerate_initial_embeddingsgenerate_permuted_embgenerate_profilesGeneWalkGeneWalkGeneratorget_aligned_embdget_db_connectionget_embeddingget_embeddingsget_gene_infoget_gene_ontology_hierarchyget_gene_ontology_infoget_gene_pathway_dtget_gene_to_goget_gene_to_reactomeget_graph_dtget_graph_dtsget_gw_dataget_gw_data_filteredget_interactions_combinedget_interactions_intactget_interactions_pcget_interactions_reactomeget_interactions_signorget_interactions_stringget_profilesget_reactome_hierarchyget_reactome_infoget_scoresget_statsinstall_agent_skillmetapath2vecn_nodesnew_data_buildernode2vecnode2vec_test_dataparams_diffusion_profilesparams_genewalkparams_genewalk_dataparams_kernelparams_metapath2vecparams_node2vecplot_gw_resultsplot_similaritiesreload_dbrs_build_synthetic_genewalkrs_cosine_simrs_differential_graph_datars_diffusers_diffusion_profilesrs_gene_walkrs_gene_walk_permrs_gene_walk_testrs_kernel_node_namesrs_metapath2vecrs_node2vecrs_node2vec_synthetic_datars_procrustes_alignrs_profile_distancessynthetic_genewalk_data

Dependencies:askpassbackportsbase64encbriobslibcachemcallrcheckmateclicpp11crosstalkcurldata.tableDBIdescdigestdplyrduckdbevaluatefarverfastmapfontawesomefsgenericsggplot2gluegridExtragtablehighrhtmltoolshtmlwidgetshttrigraphisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclemagrittrMatrixmemoisemimeopensslotelpillarpkgbuildpkgconfigplotlyprocessxpromisespspurrrR6rappdirsRColorBrewerRcpprextendrrlangrmarkdownrprojrootS7sassscalesstringistringrsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunyamlzeallot

How to run GeneWalk
Exploring Gene Walk | Setup | Synthetic data | Exploring the data and initialising the object | Running gene walk on the synthetic data | Real data | Using the builder factory | Check the node degree | Running gene walk on actual data | Exploring the results | Check the embeddings | Scatter plot | Actual data | Random data set | Using your own data
Rendered fromgenewalk.qmdusingquarto::html

Last update: 2026-10-23
Started: 2026-02-23

Diffusion profiles
Setup | Background | A toy interactome | Reactome and a MYC signature | Where does the mass go? | Comparing profiles | Choosing a metric | Caveats and next steps
Rendered fromdiffusion_profiles.qmdusingquarto::html

Last update: 2026-10-07
Started: 2026-10-07

Metapath2vec
Running metapath2vec | Setup | Background | Building a typed Reactome graph | Check your walk statistics first | Gene embeddings | Do genes cluster by biology? | Nearest neighbours | Pathway embeddings | Where to go from here
Rendered frommetapath2vec.qmdusingquarto::html

Last update: 2026-09-24
Started: 2026-09-24

Embedding Drift via node2vec
Context-aware differential embedding with node2vec | Setup | Background | Synthetic data | Visualising the two graphs | Running EmbedDrift | Initialising the object | Generating embeddings | Calculating drift
Rendered fromembedding_drift.qmdusingquarto::html

Last update: 2026-05-07
Started: 2026-03-09

Graph Diffusion
Network diffusion with genewalkR | Setup | Background | A simple example: lattice graph | Building the graph and kernel | Diffusing a single source node | Visualising score decay | Heatmap on the grid | Comparing scoring methods | Biologically motivated example: scale-free network | Generating the network | Simulating a disease gene signal | Running diffusion | Inspecting the top candidates | Comparing kernels | Summary
Rendered fromdiffusion.qmdusingquarto::html

Last update: 2026-05-07
Started: 2026-04-11

Node2vec
Running node2vec | Setup | Background | Synthetic data | Exploring node2vec | Barbell graph | Exploring the data | Cavemen graph | Stochastic blocks
Rendered fromnode2vec.qmdusingquarto::html

Last update: 2026-05-07
Started: 2026-02-23

Readme and manuals

Help Manual

Help pageTopics
Build the diffusion kernelbuild_kernel
Calculate embedding drift between two graphscalculate_drift
Calculate the pathway and gene statisticscalculate_genewalk_stats
Calculate distances between diffusion profilescalculate_profile_distances
Check the degree across different node typescheck_degree_distribution
Deduplicate edgesdedup_edges
Generate Synthetic Differential Graph Datadifferential_graph_test_data
Run diffusion scoringdiffuse_scores
DiffusionProfilesDiffusionProfiles
DiffusionScoresDiffusionScores
Download database from GitHub releasedownload_database
EmbedDriftEmbedDrift
Evaluate node2vec test resultsevaluate_node2vec_test
Generate the initial graph embeddinggenerate_initial_emb
Generate initial node embeddings for both graphsgenerate_initial_embeddings
Generate the random, permuted embeddinggenerate_permuted_emb
Generate diffusion profilesgenerate_profiles
GeneWalkGeneWalk
Gene Walk Network GeneratorGeneWalkGenerator
Get the aligned embeddingget_aligned_embd
Internal connector to the DBget_db_connection
Get the list of embeddingsget_embedding
Get node embeddingsget_embeddings
Get the gene main informationget_gene_info
Get the Gene Ontologyget_gene_ontology_hierarchy
Get the Gene Ontology main informationget_gene_ontology_info
Get the gene to pathway data.tableget_gene_pathway_dt
Get the Gene Ontology to gene connectionsget_gene_to_go
Get the Reactome to gene connectionsget_gene_to_reactome
Get the edge data.tableget_graph_dt
Get graph edge tablesget_graph_dts
Get the full GW data stored in the classget_gw_data get_gw_data.DataBuilder
Get the filtered GW data for a list of genesget_gw_data_filtered get_gw_data_filtered.DataBuilder
Get the Combined networkget_interactions_combined
Get the Intact networkget_interactions_intact
Get the pathway commons networkget_interactions_pc
Get the Reactome networkget_interactions_reactome
Get the SIGNOR networkget_interactions_signor
Get the STRING networkget_interactions_string
Get diffusion profilesget_profiles
Get the Reactome pathway hierarchyget_reactome_hierarchy
Get the Reactome main informationget_reactome_info
Get scoresget_scores
Get the statistical resultsget_stats
Install the genewalkR agent skillinstall_agent_skill
Metapath2Vecmetapath2vec
MYC target genesmyc_genes
Number of nodes representedn_nodes n_nodes.DataBuilder
Generate a new DataBuilder helper classnew_data_builder
Node2Vecnode2vec
Generate Simple Node2Vec Test Datanode2vec_test_data
Wrapper function for the diffusion profile parametersparams_diffusion_profiles
Wrapper function for the GeneWalk-specific node2vec parametersparams_genewalk
GeneWalk synthetic data paramsparams_genewalk_data
Wrapper function for the diffusion kernel parametersparams_kernel
Wrapper function for the metapath2vec parametersparams_metapath2vec
Wrapper function for the node2vec parametersparams_node2vec
Plot the gene walk resultsplot_gw_results
Plot similarity distributionsplot_similarities
Clean the cache and download the DB againreload_db
Generate synthetic GeneWalk data with controlled signal structurers_build_synthetic_genewalk
Cosine similarity between two vectorsrs_cosine_sim
Generate a synthetic differential graph pair for testing context-aware node embeddingsrs_differential_graph_data
Run diffusion scoring on a precomputed kernelrs_diffuse
Build the diffusion kernel from sparse adjacency componentsrs_diffusion_kernel
Generate diffusion profilesrs_diffusion_profiles
Generate GeneWalk node embeddings (multiple reps)rs_gene_walk
Generate null distributions from degree-matched random networksrs_gene_walk_perm
Calculate GeneWalk test statisticsrs_gene_walk_test
Pull out the node names from the kernelrs_kernel_node_names
Generate metapath2vec embeddingsrs_metapath2vec
Generate a node2vec embeddingsrs_node2vec
Generate synthetic data for node2vecrs_node2vec_synthetic_data
Orthogonal Procrustes alignment and cosine similarity scoringrs_procrustes_align
Distances between the columns of two matricesrs_profile_distances
Generate synthetic GeneWalk datasynthetic_genewalk_data