{"id":13681201,"url":"https://github.com/pnnl/leapR","last_synced_at":"2025-04-30T03:30:48.203Z","repository":{"id":44882463,"uuid":"309479090","full_name":"pnnl/leapR","owner":"pnnl","description":null,"archived":false,"fork":false,"pushed_at":"2024-12-09T18:23:02.000Z","size":51303,"stargazers_count":17,"open_issues_count":17,"forks_count":6,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-04-12T05:13:45.540Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/pnnl.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2020-11-02T19:51:43.000Z","updated_at":"2024-04-15T15:47:08.000Z","dependencies_parsed_at":"2025-04-12T05:13:49.934Z","dependency_job_id":"4163a0ca-83e0-453f-b869-e9676c10ad68","html_url":"https://github.com/pnnl/leapR","commit_stats":null,"previous_names":["pnnl/leapr","pnnl-compbio/leapr"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pnnl%2FleapR","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pnnl%2FleapR/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pnnl%2FleapR/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pnnl%2FleapR/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/pnnl","download_url":"https://codeload.github.com/pnnl/leapR/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":251635028,"owners_count":21619129,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-08-02T13:01:27.730Z","updated_at":"2025-04-30T03:30:43.195Z","avatar_url":"https://github.com/pnnl.png","language":"R","funding_links":[],"categories":["7. Protein Pathway Enrichment"],"sub_categories":["Table of Contents"],"readme":"#leapR\n\nLayered Enrichment Analysis of Pathways in R (leapR) a tool that carries out statistical enrichment analysis on single- or multi-omics data.\n\n## Installation\nTo install leapR, you can use the `devtools` package as follows:\n\n``` R\ninstall.packages(\"devtools\")\ndevtools::install_github(\"PNNL-CompBio/leapR\",build_vignette=TRUE)\n```\n\nOnce you have successfully installed the package you can load the vignette to read examples using the `vignette('leapR')` command.\n\n## Basic Usage\n\nThe primary function of the `leapR` package is the `leapR` function itself. This function serves a wrapper to run different styles of enrichment functions on the data. The package contains other functions to support pathway information and multi-omics datasets.\n\n### Enrichment calls\n\nHere is a list of enrichment arguments that can be called with the `leapR` command.\n\n| Argument                                        | Description |   \n| ---                                             | ----        |   \n| `enrichment_in_sets`                           | Calculates enrichment in pathway membership in a list (e.g. highly differential proteins) relative to background using Fisher's exact test. |   \n| `enrichment_in_order`                         | Calculates enrichment of pathways based on a ranked list using the Kologmorov-Smirnov test |   \n| `enrichment_comparison`                         | Compares the distribution of abundances between two sets of conditions for each pathway using a t test  |\n| `enrichment_in_pathways`                        | Compares the distribution of abundances in a pathway with the background distribution of abundances using a t test |   \n|`correlation_enrichment`              | Calculates the enrichment of a pathway based on correlation between pathway members across conditions versus correlation between members not in the pathway             |   \n| `enrichment_in_relationships`| Calculates the enrichment of a pathway in specified interactions relative to non-pathway members |\n\n### Data examples\nWe included examples of including proteomics data and transcriptomics data from 169 high-grade serous ovarian cancer (HGSOC) tumors previously studied and lists of the short- and long- surviving patients from that cohort.\n\n### Gene pathway examples\nWe included two different gene pathways. An NCI pathway database (Pathway Information Database; PID) of signaling pathways and the MSIGDB set of gene collections from various sources.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpnnl%2FleapR","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpnnl%2FleapR","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpnnl%2FleapR/lists"}