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pathfindR
View on CRAN: Click
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Download and install pathfindR package within the R console
Install from CRAN:
install.packages("pathfindR")
Install from Github:
library("remotes")
install_github("cran/pathfindR")
Install by package version:
library("remotes")
install_version("pathfindR", "2.4.1")
Attach the package and use:
library("pathfindR")
Maintained by
Ege Ulgen
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2018-03-09
Latest Update: 2024-01-19
Description:
Enrichment analysis enables researchers to uncover mechanisms
underlying a phenotype. However, conventional methods for enrichment
analysis do not take into account protein-protein interaction information,
resulting in incomplete conclusions. pathfindR is a tool for enrichment
analysis utilizing active subnetworks. The main function identifies active
subnetworks in a protein-protein interaction network using a user-provided
list of genes and associated p values. It then performs enrichment analyses
on the identified subnetworks, identifying enriched terms (i.e. pathways or,
more broadly, gene sets) that possibly underlie the phenotype of interest.
pathfindR also offers functionalities to cluster the enriched terms and
identify representative terms in each cluster, to score the enriched terms
per sample and to visualize analysis results. The enrichment, clustering and
other methods implemented in pathfindR are described in detail in
Ulgen E, Ozisik O, Sezerman OU. 2019. pathfindR: An R Package for
Comprehensive Identification of Enriched Pathways in Omics Data Through
Active Subnetworks. Front. Genet. .
How to cite:
Ege Ulgen (2018). pathfindR: Enrichment Analysis Utilizing Active Subnetworks. R package version 2.4.1, https://cran.r-project.org/web/packages/pathfindR. Accessed 05 Jan. 2025.
Previous versions and publish date:
1.0.0 (2018-03-09 13:18), 1.1.0 (2018-05-15 00:43), 1.2.0 (2018-06-10 15:24), 1.2.1 (2018-08-18 00:10), 1.2.2 (2018-10-05 01:00), 1.2.3 (2018-10-26 16:40), 1.3.0 (2018-11-20 12:10), 1.4.0 (2019-11-08 12:40), 1.4.1 (2019-11-15 12:10), 1.4.2 (2019-12-06 12:30), 1.5.0 (2020-06-07 02:00), 1.5.1 (2020-09-20 20:00), 1.6.0 (2020-11-21 14:50), 1.6.1 (2021-01-04 20:40), 1.6.2 (2021-08-21 15:20), 1.6.3 (2021-11-15 10:20), 1.6.4 (2022-08-25 14:30), 2.0.0 (2023-05-06 06:20), 2.0.1 (2023-05-10 09:40), 2.1.0 (2023-05-12 09:10), 2.2.0 (2023-08-21 02:40), 2.3.0 (2023-10-08 22:30), 2.3.1 (2024-01-19 20:10), 2.4.0 (2024-04-28 13:50)
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imports, suggests or enhances
Complete documentation for pathfindR
Functions, R codes and Examples using
the pathfindR R package
Some associated functions: UpSet_plot . active_snw_enrichment_wrapper . active_snw_search . annotate_term_genes . check_java_version . cluster_enriched_terms . cluster_graph_vis . color_kegg_pathway . combine_pathfindR_results . combined_results_graph . configure_output_dir . create_HTML_report . create_kappa_matrix . download_KGML_file . download_kegg_png . enrichment . enrichment_analyses . enrichment_chart . fetch_gene_set . fetch_java_version . filterActiveSnws . fuzzy_term_clustering . get_biogrid_pin . get_gene_sets_list . get_kegg_gsets . get_mgsigdb_gsets . get_pin_file . get_reactome_gsets . gset_list_from_gmt . hierarchical_term_clustering . hyperg_test . input_processing . input_testing . isColor . obtain_colored_url . pathfindR . plot_scores . process_pin . return_pin_path . run_pathfindR . score_terms . single_iter_wrapper . summarize_enrichment_results . term_gene_graph . term_gene_heatmap . visualize_active_subnetworks . visualize_hsa_KEGG . visualize_term_interactions . visualize_terms .
Some associated R codes: active_snw_search.R . clustering.R . comparison.R . core.R . data_generation.R . enrichment.R . pathfindr.R . scoring.R . utility.R . visualization.R . zzz.R . Full pathfindR package functions and examples
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