Files in saezlab/OmnipathR
OmniPath web service client and more

.Rbuildignore

.bumpversion.cfg

.github/workflows/install_by_pak.yaml

.gitignore

DESCRIPTION

LICENSE

NAMESPACE

NEWS.md R/aaa.R R/adecorate.R R/adecorators.R R/annotate_network.R R/annotations.R R/bioplex.R R/bma.R R/cache.R R/chalmers_gem.R R/complexes.R R/complexes_genes.R R/consensuspathdb.R R/cookie.R R/cosmos.R R/dbmanager.R R/ensembl.R R/entity.R R/enz_sub.R R/evex.R R/evidences.R R/extra_attrs.R R/go.R R/graph.R R/guide2pharma.R R/harmonizome.R R/hmdb.R R/homologene.R R/homology.R R/hpo.R R/htridb.R R/id_mapping.R R/inbiomap.R R/interactions.R R/intercell.R R/intercell_curated.R R/internals.R R/kegg.R R/log.R R/misc.R R/netvis.R R/nichenet.R R/obo.R R/oma.R R/omnipath.R R/omnipathr.R R/ontology.R R/options.R R/orthology.R R/pathwaycommons.R R/preppi.R R/print_interactions.R R/ramilowski.R R/ramp.R R/regnetwork.R R/remap.R R/resources.R R/search.R R/static.R R/stitch.R

R/sysdata.rda

R/taxonomy.R R/tfcensus.R R/trrust.R R/uniprot.R R/utils.R R/vinayagam.R R/xml.R R/zenodo.R R/zzz.R README.md

_pkgdown.yml

docs/404.html

docs/CNAME

docs/LICENSE-text.html

docs/apple-touch-icon-120x120.png

docs/apple-touch-icon-152x152.png

docs/apple-touch-icon-180x180.png

docs/apple-touch-icon-60x60.png

docs/apple-touch-icon-76x76.png

docs/apple-touch-icon.png

docs/articles/bioc_workshop.html

docs/articles/bioc_workshop_files/header-attrs-2.9.5/header-attrs.js

docs/articles/cosmos.html

docs/articles/db_manager.html

docs/articles/drug_targets.html

docs/articles/drug_targets_files/figure-html/unnamed-chunk-12-1.png

docs/articles/drug_targets_files/header-attrs-2.9.5/header-attrs.js

docs/articles/extra_attrs.html

docs/articles/gene_ontology.html

docs/articles/gene_ontology_files/header-attrs-2.9.5/header-attrs.js

docs/articles/index.html

docs/articles/nichenet.html

docs/articles/nichenet_files/header-attrs-2.9.5/header-attrs.js

docs/articles/omnipath_intro.html

docs/articles/paths.html

docs/articles/paths_files/header-attrs-2.9.5/header-attrs.js

docs/authors.html

docs/deps/bootstrap-5.3.1/bootstrap.bundle.min.js

docs/deps/bootstrap-5.3.1/bootstrap.min.css

docs/deps/bootstrap-5.3.1/font.css

docs/deps/bootstrap-5.3.1/fonts/6xK3dSBYKcSV-LCoeQqfX1RYOo3aPA.woff

docs/deps/bootstrap-5.3.1/fonts/6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vAkw.woff

docs/deps/bs3compat-0.2.5.1/bs3compat.js

docs/deps/bs3compat-0.2.5.1/tabs.js

docs/deps/data-deps.txt

docs/deps/jquery-3.6.0/jquery-3.6.0.js

docs/deps/jquery-3.6.0/jquery-3.6.0.min.js

docs/deps/jquery-3.6.0/jquery-3.6.0.min.map

docs/extra.css

docs/favicon-16x16.png

docs/favicon-32x32.png

docs/favicon.ico

docs/index.html

docs/link.svg

docs/logo.svg

docs/news/index.html

docs/package-logo.png

docs/pkgdown.css

docs/pkgdown.js

docs/pkgdown.yml

docs/reference/OmnipathR.html

docs/reference/Rplot001.png

docs/reference/all_uniprot_acs.html

docs/reference/all_uniprots.html

docs/reference/ancestors.html

docs/reference/annotated_network.html

docs/reference/annotation_categories.html

docs/reference/annotation_resources.html

docs/reference/annotations.html

docs/reference/biomart_query.html

docs/reference/bioplex1.html

docs/reference/bioplex2.html

docs/reference/bioplex3.html

docs/reference/bioplex_all.html

docs/reference/bioplex_hct116_1.html

docs/reference/bma_motif_es.html

docs/reference/bma_motif_vs.html

docs/reference/chalmers_gem.html

docs/reference/chalmers_gem_id_mapping_table.html

docs/reference/chalmers_gem_id_type.html

docs/reference/chalmers_gem_metabolites.html

docs/reference/chalmers_gem_network.html

docs/reference/chalmers_gem_raw.html

docs/reference/chalmers_gem_reactions.html

docs/reference/collectri.html

docs/reference/common_name.html

docs/reference/complex_genes.html

docs/reference/complex_resources.html

docs/reference/complexes.html

docs/reference/consensuspathdb_download.html

docs/reference/consensuspathdb_raw_table.html

docs/reference/cookie.html

docs/reference/cosmos_pkn.html

docs/reference/curated_ligand_receptor_interactions.html

docs/reference/curated_ligrec_stats.html

docs/reference/database_summary.html

docs/reference/datasets_one_column.html

docs/reference/descendants.html

docs/reference/dorothea.html

docs/reference/dot-omnipath_options_defaults.html

docs/reference/dot-omnipathr_options_defaults.html

docs/reference/ensembl_dataset.html

docs/reference/ensembl_homology.html

docs/reference/ensembl_id_mapping_table.html

docs/reference/ensembl_id_type.html

docs/reference/ensembl_name.html

docs/reference/ensembl_organisms.html

docs/reference/ensembl_organisms_raw.html

docs/reference/ensembl_orthology.html

docs/reference/ensure_igraph.html

docs/reference/enzsub_graph.html

docs/reference/enzsub_resources.html

docs/reference/enzyme_substrate.html

docs/reference/evex_download.html

docs/reference/evidences.html

docs/reference/extra_attr_to_column.html

docs/reference/extra_attr_values.html

docs/reference/extra_attrs.html

docs/reference/extra_attrs_to_cols.html

docs/reference/figures/logo_omnipath.png

docs/reference/figures/page1_1.png

docs/reference/filter_by_resource.html

docs/reference/filter_evidences.html

docs/reference/filter_extra_attrs.html

docs/reference/filter_intercell.html

docs/reference/filter_intercell_network.html

docs/reference/find_all_paths.html

docs/reference/foo/bar/circadian.png

docs/reference/foo/bar/hsa04710.png

docs/reference/from_evidences.html

docs/reference/get_annotation_resources.html

docs/reference/get_complex_genes.html

docs/reference/get_complex_resources.html

docs/reference/get_db.html

docs/reference/get_enzsub_resources.html

docs/reference/get_interaction_resources.html

docs/reference/get_intercell_categories.html

docs/reference/get_intercell_generic_categories.html

docs/reference/get_intercell_resources.html

docs/reference/get_ontology_db.html

docs/reference/get_resources.html

docs/reference/get_signed_ptms.html

docs/reference/giant_component.html

docs/reference/go_annot_download.html

docs/reference/go_annot_slim.html

docs/reference/go_ontology_download.html

docs/reference/graph_interaction.html

docs/reference/guide2pharma_download.html

docs/reference/harmonizome_download.html

docs/reference/has_extra_attrs.html

docs/reference/hmdb_id_mapping_table.html

docs/reference/hmdb_id_type.html

docs/reference/hmdb_metabolite_fields.html

docs/reference/hmdb_protein_fields.html

docs/reference/hmdb_table.html

docs/reference/homologene_download.html

docs/reference/homologene_organisms.html

docs/reference/homologene_raw.html

docs/reference/homologene_uniprot_orthology.html

docs/reference/homology_translate.html

docs/reference/hpo_download.html

docs/reference/hsa04710.png

docs/reference/htridb_download.html

docs/reference/id_translation_resources.html

docs/reference/id_types.html

docs/reference/import_all_interactions.html

docs/reference/import_dorothea_interactions.html

docs/reference/import_intercell_network.html

docs/reference/import_kinaseextra_interactions.html

docs/reference/import_ligrecextra_interactions.html

docs/reference/import_lncrna_mrna_interactions.html

docs/reference/import_mirnatarget_interactions.html

docs/reference/import_omnipath_annotations.html

docs/reference/import_omnipath_complexes.html

docs/reference/import_omnipath_enzsub.html

docs/reference/import_omnipath_interactions.html

docs/reference/import_omnipath_intercell.html

docs/reference/import_pathwayextra_interactions.html

docs/reference/import_post_translational_interactions.html

docs/reference/import_small_molecule_protein_interactions.html

docs/reference/import_tf_mirna_interactions.html

docs/reference/import_tf_target_interactions.html

docs/reference/import_transcriptional_interactions.html

docs/reference/inbiomap_download.html

docs/reference/inbiomap_raw.html

docs/reference/index.html

docs/reference/interaction_datasets.html

docs/reference/interaction_graph.html

docs/reference/interaction_resources.html

docs/reference/interaction_types.html

docs/reference/intercell.html

docs/reference/intercell_categories.html

docs/reference/intercell_consensus_filter.html

docs/reference/intercell_generic_categories.html

docs/reference/intercell_network.html

docs/reference/intercell_resources.html

docs/reference/intercell_summary.html

docs/reference/is_ontology_id.html

docs/reference/is_swissprot.html

docs/reference/is_trembl.html

docs/reference/is_uniprot.html

docs/reference/kegg_info.html

docs/reference/kegg_open.html

docs/reference/kegg_pathway_annotations.html

docs/reference/kegg_pathway_download.html

docs/reference/kegg_pathway_list.html

docs/reference/kegg_pathways_download.html

docs/reference/kegg_picture.html

docs/reference/kegg_process.html

docs/reference/latin_name.html

docs/reference/load_db.html

docs/reference/ncbi_taxid.html

docs/reference/nichenet_build_model.html

docs/reference/nichenet_expression_data.html

docs/reference/nichenet_gr_network.html

docs/reference/nichenet_gr_network_evex.html

docs/reference/nichenet_gr_network_harmonizome.html

docs/reference/nichenet_gr_network_htridb.html

docs/reference/nichenet_gr_network_omnipath.html

docs/reference/nichenet_gr_network_pathwaycommons.html

docs/reference/nichenet_gr_network_regnetwork.html

docs/reference/nichenet_gr_network_remap.html

docs/reference/nichenet_gr_network_trrust.html

docs/reference/nichenet_ligand_activities.html

docs/reference/nichenet_ligand_target_links.html

docs/reference/nichenet_ligand_target_matrix.html

docs/reference/nichenet_lr_network.html

docs/reference/nichenet_lr_network_guide2pharma.html

docs/reference/nichenet_lr_network_omnipath.html

docs/reference/nichenet_lr_network_ramilowski.html

docs/reference/nichenet_main.html

docs/reference/nichenet_networks.html

docs/reference/nichenet_optimization.html

docs/reference/nichenet_remove_orphan_ligands.html

docs/reference/nichenet_results/networks.rds

docs/reference/nichenet_results_dir.html

docs/reference/nichenet_signaling_network.html

docs/reference/nichenet_signaling_network_cpdb.html

docs/reference/nichenet_signaling_network_evex.html

docs/reference/nichenet_signaling_network_harmonizome.html

docs/reference/nichenet_signaling_network_inbiomap.html

docs/reference/nichenet_signaling_network_omnipath.html

docs/reference/nichenet_signaling_network_pathwaycommons.html

docs/reference/nichenet_signaling_network_vinayagam.html

docs/reference/nichenet_test.html

docs/reference/nichenet_workarounds.html

docs/reference/obo_parser.html

docs/reference/oma_code.html

docs/reference/oma_organisms.html

docs/reference/oma_pairwise.html

docs/reference/oma_pairwise_genesymbols.html

docs/reference/oma_pairwise_translated.html

docs/reference/omnipath-interactions.html

docs/reference/omnipath.html

docs/reference/omnipath_cache_autoclean.html

docs/reference/omnipath_cache_clean.html

docs/reference/omnipath_cache_clean_db.html

docs/reference/omnipath_cache_download_ready.html

docs/reference/omnipath_cache_filter_versions.html

docs/reference/omnipath_cache_get.html

docs/reference/omnipath_cache_key.html

docs/reference/omnipath_cache_latest_or_new.html

docs/reference/omnipath_cache_latest_version.html

docs/reference/omnipath_cache_load.html

docs/reference/omnipath_cache_move_in.html

docs/reference/omnipath_cache_remove.html

docs/reference/omnipath_cache_save.html

docs/reference/omnipath_cache_search.html

docs/reference/omnipath_cache_set_ext.html

docs/reference/omnipath_cache_update_status.html

docs/reference/omnipath_cache_wipe.html

docs/reference/omnipath_config_path.html

docs/reference/omnipath_for_cosmos.html

docs/reference/omnipath_get_config_path.html

docs/reference/omnipath_load_config.html

docs/reference/omnipath_log.html

docs/reference/omnipath_logfile.html

docs/reference/omnipath_msg.html

docs/reference/omnipath_query.html

docs/reference/omnipath_reset_config.html

docs/reference/omnipath_save_config.html

docs/reference/omnipath_set_cachedir.html

docs/reference/omnipath_set_console_loglevel.html

docs/reference/omnipath_set_logfile_loglevel.html

docs/reference/omnipath_set_loglevel.html

docs/reference/omnipath_show_db.html

docs/reference/omnipath_unlock_cache_db.html

docs/reference/only_from.html

docs/reference/ontology_ensure_id.html

docs/reference/ontology_ensure_name.html

docs/reference/ontology_name_id.html

docs/reference/organism_for.html

docs/reference/orthology_translate.html

docs/reference/orthology_translate_column.html

docs/reference/pathwaycommons_download.html

docs/reference/pivot_annotations.html

docs/reference/preppi_download.html

docs/reference/preppi_filter.html

docs/reference/print_bma_motif_es.html

docs/reference/print_bma_motif_vs.html

docs/reference/print_interactions.html

docs/reference/print_path_es.html

docs/reference/print_path_vs.html

docs/reference/pubmed_open.html

docs/reference/query_info.html

docs/reference/ramilowski_download.html

docs/reference/ramp_id_mapping_table.html

docs/reference/ramp_id_type.html

docs/reference/ramp_sqlite.html

docs/reference/ramp_table.html

docs/reference/ramp_tables.html

docs/reference/regnetwork_directions.html

docs/reference/regnetwork_download.html

docs/reference/relations_list_to_table.html

docs/reference/relations_table_to_graph.html

docs/reference/relations_table_to_list.html

docs/reference/remap_dorothea_download.html

docs/reference/remap_filtered.html

docs/reference/remap_tf_target_download.html

docs/reference/resource_info.html

docs/reference/resources.html

docs/reference/resources_colname.html

docs/reference/resources_in.html

docs/reference/search_omnipath.html

docs/reference/show_network.html

docs/reference/signed_ptms.html

docs/reference/simplify_intercell_network.html

docs/reference/static_table.html

docs/reference/static_tables.html

docs/reference/stitch_actions.html

docs/reference/stitch_gem.html

docs/reference/stitch_links.html

docs/reference/stitch_network.html

docs/reference/stitch_remove_prefixes.html

docs/reference/subnetwork.html

docs/reference/swap_relations.html

docs/reference/swissprots_only.html

docs/reference/tfcensus_download.html

docs/reference/translate_ids.html

docs/reference/translate_ids_multi.html

docs/reference/trembls_only.html

docs/reference/trrust_download.html

docs/reference/uniprot_full_id_mapping_table.html

docs/reference/uniprot_genesymbol_cleanup.html

docs/reference/uniprot_id_mapping_table.html

docs/reference/uniprot_id_type.html

docs/reference/uniprot_idmapping_id_types.html

docs/reference/unique_intercell_network.html

docs/reference/unnest_evidences.html

docs/reference/uploadlists_id_type.html

docs/reference/vinayagam_download.html

docs/reference/walk_ontology_tree.html

docs/reference/with_extra_attrs.html

docs/reference/with_references.html

docs/reference/zenodo_download.html

docs/search.json

docs/sitemap.xml

docs/syntax-highlighting.css

inst/CITATION

inst/db/db_def.json

inst/internal/biomart.xml

inst/internal/entity_types.yaml

inst/internal/id_types.json

inst/internal/magic_bytes.json

inst/internal/organisms.yaml

inst/internal/urls.json

logo.svg

man/OmnipathR.Rd man/all_uniprot_acs.Rd man/all_uniprots.Rd man/ancestors.Rd man/annotated_network.Rd man/annotation_categories.Rd man/annotation_resources.Rd man/annotations.Rd man/biomart_query.Rd man/bioplex1.Rd man/bioplex2.Rd man/bioplex3.Rd man/bioplex_all.Rd man/bioplex_hct116_1.Rd man/bma_motif_es.Rd man/bma_motif_vs.Rd man/chalmers_gem.Rd man/chalmers_gem_id_mapping_table.Rd man/chalmers_gem_id_type.Rd man/chalmers_gem_metabolites.Rd man/chalmers_gem_network.Rd man/chalmers_gem_raw.Rd man/chalmers_gem_reactions.Rd man/common_name.Rd man/complex_genes.Rd man/complex_resources.Rd man/complexes.Rd man/consensuspathdb_download.Rd man/consensuspathdb_raw_table.Rd man/cookie.Rd man/cosmos_pkn.Rd man/curated_ligand_receptor_interactions.Rd man/curated_ligrec_stats.Rd man/database_summary.Rd man/datasets_one_column.Rd man/descendants.Rd man/dot-omnipathr_options_defaults.Rd man/ensembl_dataset.Rd man/ensembl_id_mapping_table.Rd man/ensembl_id_type.Rd man/ensembl_name.Rd man/ensembl_organisms.Rd man/ensembl_organisms_raw.Rd man/ensembl_orthology.Rd man/ensure_igraph.Rd man/enzsub_graph.Rd man/enzsub_resources.Rd man/enzyme_substrate.Rd man/evex_download.Rd man/evidences.Rd man/extra_attr_values.Rd man/extra_attrs.Rd man/extra_attrs_to_cols.Rd

man/figures/logo_omnipath.png

man/figures/page1_1.png

pkgdown/extra.css

pkgdown/favicon/apple-touch-icon-120x120.png

pkgdown/favicon/apple-touch-icon-152x152.png

pkgdown/favicon/apple-touch-icon-180x180.png

pkgdown/favicon/apple-touch-icon-60x60.png

pkgdown/favicon/apple-touch-icon-76x76.png

pkgdown/favicon/apple-touch-icon.png

pkgdown/favicon/favicon-16x16.png

pkgdown/favicon/favicon-32x32.png

pkgdown/favicon/favicon.ico

tests/testthat.R tests/testthat/test_import.R

vignettes/.gitignore

vignettes/Bioc.bib

vignettes/author-info-blocks.lua

vignettes/bioc_workshop.Rmd vignettes/cosmos.Rmd vignettes/db_manager.Rmd vignettes/drug_targets.Rmd vignettes/extra_attrs.Rmd

vignettes/man/figures/fig2-1.png

vignettes/man/figures/fig3-1.png

vignettes/man/figures/fig4-1.png

vignettes/man/figures/page1_1.png

vignettes/nichenet.Rmd vignettes/omnipath_intro.Rmd vignettes/paths.Rmd

vignettes/scholarly-metadata.lua

saezlab/OmnipathR documentation built on Nov. 10, 2024, 11:02 p.m.

rdrr.io home R language documentation Run R code online

CRAN packages Bioconductor packages R-Forge packages GitHub packages

Note that we can't provide technical support on individual packages. You should contact the package authors for that.

saezlab/OmnipathR
OmniPath web service client and more

Files in saezlab/OmnipathR
OmniPath web service client and more

R Package Documentation

Browse R Packages

We want your feedback!

saezlab/OmnipathR OmniPath web service client and more

Files in saezlab/OmnipathR OmniPath web service client and more

R Package Documentation

Browse R Packages

We want your feedback!

saezlab/OmnipathR
OmniPath web service client and more

Files in saezlab/OmnipathR
OmniPath web service client and more