{"doi":"10.1093/bioadv/vbad009","title":"IntLIM 2.0: identifying multi-omic relationships dependent on discrete or continuous phenotypic measurements","abstract":"Motivation: IntLIM uncovers phenotype-dependent linear associations between two types of analytes (e.g. genes and metabolites) in a multi-omic dataset, which may reflect chemically or biologically relevant relationships. Results: The new IntLIM R package includes newly added support for generalized data types, covariate correction, continuous phenotypic measurements, model validation and unit testing. IntLIM analysis uncovered biologically relevant gene-metabolite associations in two separate datasets, and the run time is improved over baseline R functions by multiple orders of magnitude. Availability and implementation: IntLIM is available as an R package with a detailed vignette (https://github.com/ncats/IntLIM) and as an R Shiny app (see Supplementary Figs S1-S6) (https://intlim.ncats.io/). Supplementary information: online.","journal":"Bioinformatics Advances","year":2023,"id":374188,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":4,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.8148,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":859200,"name":"Kyle Spencer","orcid":"0000-0002-6720-5348","position":1,"is_corresponding":false},{"id":784950,"name":"Jalal Siddiqui","orcid":"0000-0002-5100-6432","position":2,"is_corresponding":false},{"id":367400,"name":"Raghu Machiraju","orcid":"0000-0002-8101-8119","position":3,"is_corresponding":false},{"id":37894,"name":"Ewy A. Mathé","orcid":"0000-0003-4491-8107","position":4,"is_corresponding":false},{"id":550313,"name":"Tara Eicher","orcid":"0000-0003-1809-4458","position":0,"is_corresponding":true}],"reference_count":18,"raw_metadata":null,"created_at":"2026-07-19T01:16:11.341687Z","pmid":"36922980","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}