{"doi":"10.1093/bioinformatics/btn129","title":"<i>adegenet</i>: a R package for the multivariate analysis of genetic markers","abstract":"<jats:title>Abstract</jats:title><jats:p>Summary: The package adegenet for the R software is dedicated to the multivariate analysis of genetic markers. It extends the ade4 package of multivariate methods by implementing formal classes and functions to manipulate and analyse genetic markers. Data can be imported from common population genetics software and exported to other software and R packages. adegenet also implements standard population genetics tools along with more original approaches for spatial genetics and hybridization.</jats:p><jats:p>Availability: Stable version is available from CRAN: http://cran.r-project.org/mirrors.html. Development version is available from adegenet website: http://adegenet.r-forge.r-project.org/. Both versions can be installed directly from R. adegenet is distributed under the GNU General Public Licence (v.2).</jats:p><jats:p>Contact:  jombart@biomserv.univ-lyon1.fr</jats:p><jats:p>Supplementary information:  Supplementary data are available at Bioinformatics online.</jats:p>","journal":"Bioinformatics","year":2008,"id":3662,"datarank":1.3469124950014517,"base_score":8.97941663334301,"endowment":8.97941663334301,"self_citation_contribution":1.3469124950014517,"citation_network_contribution":0.0,"self_endowment_contribution":1.3469124950014517,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":7937,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.0556,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2008-04-08","fair_score":55.0,"fair_percentile":80.29903254177661,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":37446,"name":"Thibaut Jombart","orcid":"0000-0003-2226-8692","position":0,"is_corresponding":true}],"reference_count":17,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-03-01T18:20:47.508186Z","pmid":null,"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":100.0,"fair_a":70.0,"fair_i":50.0,"fair_r":0.0,"fair_zscore":0.8854,"fair_rationale":{"fair_score":55.0,"has_llm":false,"dimensions":{"F":{"name":"Findable","score":100.0,"criteria":[{"key":"f_has_doi","label":"Has a persistent DOI","kind":"deterministic","weight":1.0,"fraction":1.0,"signal":"DOI present","rationale":null},{"key":"f_repository_presence","label":"Indexed in repositories / literature DBs","kind":"deterministic","weight":1.0,"fraction":1.0,"signal":"datacite=25, pmcid=False, pmid=True","rationale":null},{"key":"f_persistent_ids","label":"Resolvable scholarly identifiers (OpenAlex)","kind":"deterministic","weight":0.5,"fraction":1.0,"signal":"OpenAlex id present","rationale":null}]},"A":{"name":"Accessible","score":70.0,"criteria":[{"key":"a_open_access","label":"Open Access / files deposited","kind":"deterministic","weight":1.5,"fraction":0.5,"signal":"files/OA location present but not flagged OA","rationale":null},{"key":"a_retrievable","label":"Free full text retrievable","kind":"deterministic","weight":1.0,"fraction":1.0,"signal":"4 OA location(s)","rationale":null}]},"I":{"name":"Interoperable","score":50.0,"criteria":[{"key":"i_linked_data","label":"Linked datasets / DataCite relations","kind":"deterministic","weight":1.0,"fraction":1.0,"signal":"linked_datasets=25, datacite=25","rationale":null},{"key":"i_standard_ids","label":"References data via standard accessions","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"accessions=0, trials=0","rationale":null}]},"R":{"name":"Reusable","score":0.0,"criteria":[{"key":"r_license","label":"Clear, open reuse license","kind":"deterministic","weight":1.5,"fraction":0.0,"signal":"no license","rationale":null},{"key":"r_downloads","label":"Demonstrated reuse (downloads)","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"downloads=0","rationale":null},{"key":"r_version","label":"Versioned / maintained","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"no version chain","rationale":null},{"key":"r_dataset","label":"Classified as a data resource","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"not a dataset","rationale":null}]}},"suggestions":["Attach a clear, open reuse license (e.g. CC-BY or CC0).","Reference data using standard accessions (e.g. GEO, PDB, ClinicalTrials.gov).","Maintain explicit versioning for the dataset.","Make the paper/data Open Access or deposit the files in an open repository."],"model":null,"agent_version":"fair_agent_v1","fulltext_source":"abstract_only"},"fair_model":null,"fair_agent_version":"fair_agent_v1","fair_fulltext_source":"abstract_only","fair_has_llm":false,"fair_computed_at":"2026-06-11T01:47:16.041337Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}