ArticleBioinformatics (Oxford, England)2016
genipe: an automated genome-wide imputation pipeline with automatic reporting and statistical tools.
Article in Bioinformatics (Oxford, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers, 2 of them syntheses that pooled it.
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
19 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Assessment of the functionality and usability of open-source rare variant analysis pipelines.Briefings in bioinformatics · 2025Pooled it
- Genetic meta-analysis of cancer diagnosis following statin use identifies new associations and implicates human leukocyte antigen (HLA) in women.The pharmacogenomics journal · 2021Pooled it
- Genomic Investigation of Remission and Relapse of Psychotic Depression Treated with Sertraline plus Olanzapine: The STOP-PD II Study.Neuropsychobiology · 2023Trial
- Identification of candidate genes and pathways in retinopathy of prematurity by whole exome sequencing of preterm infants enriched in phenotypic extremes.Scientific reports · 2021Trial
- Meta-sGWAS: Integrating brain spatial interactions to uncover genetic variants in Bipolar Disorder.Research square · 2025Article
- Genomic dissection of sleep archetypes in a large autism cohort.medRxiv : the preprint server for health sciences · 2025Article
- Analysis of follow-up data in large biobank cohorts: a review of methodology.Frontiers in genetics · 2025Article
- Polygenic score analyses on antidepressant response in late-life depression, results from the IRL-GRey study.The pharmacogenomics journal · 2024Article
- Susceptibility gene identification and risk evaluation model construction by transcriptome-wide association analysis for salt sensitivity of blood pressure.BMC genomics · 2024Article
- Gut microbial diversity moderates polygenic risk of schizophrenia.Frontiers in psychiatry · 2024Article
- Exploratory genome-wide analyses of cortical inhibition, facilitation, and plasticity in late-life depression.Translational psychiatry · 2023Article
- BIGwas: Single-command quality control and association testing for multi-cohort and biobank-scale GWAS/PheWAS data.GigaScience · 2021Article
- Genetic and morphological estimates of androgen exposure predict social deficits in multiple neurodevelopmental disorder cohorts.Molecular autism · 2021Article
- Gene-Based Testing of Interactions Using XGBoost in Genome-Wide Association Studies.Frontiers in cell and developmental biology · 2021Article
- Estimating the Prevalence and Genetic Risk Mechanisms of ARFID in a Large Autism Cohort.Frontiers in psychiatry · 2021Article
- A Fast and Accurate Method for Genome-Wide Time-to-Event Data Analysis and Its Application to UK Biobank.American journal of human genetics · 2020Article
- Odyssey: a semi-automated pipeline for phasing, imputation, and analysis of genome-wide genetic data.BMC bioinformatics · 2019Article
- Open Humans: A platform for participant-centered research and personal data exploration.GigaScience · 2019Review
- gwasurvivr: an R package for genome-wide survival analysis.Bioinformatics (Oxford, England) · 2019Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genotype imputation is now commonly performed following genome-wide genotyping experiments. Imputation increases the density of analyzed genotypes in the dataset, enabling fine-mapping across the genome. However, the process of imputation using the most recent publicly available reference datasets can require considerable computation power and the management of hundreds of large intermediate files. We have developed genipe, a complete genome-wide imputation pipeline which includes automatic reporting, imputed data indexing and management, and a suite of statistical tests for imputed data commonly used in genetic epidemiology (Sequence Kernel Association Test, Cox proportional hazards for survival analysis, and linear mixed models for repeated measurements in longitudinal studies). AVAILABILITY AND IMPLEMENTATION: The genipe package is an open source Python software and is freely available for non-commercial use (CC BY-NC 4.0) at https://github.com/pgxcentre/genipe Documentation and tutorials are available at http://pgxcentre.github.io/genipe CONTACT: louis-philippe.lemieux.perreault@statgen.org or marie-pierre.dube@statgen.orgSupplementary information: Supplementary data are available at Bioinformatics online.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.