Computational and Analytical Tool
Name |
Description |
Ref (PMID) |
LEADER |
CelL sEletion viA aDaptivE Reweighting Method to subset cells aiming to capture rare cell types with the goal of creating more balanced datasets. Leader requires a processed seurat object with gene expression data and an optional marker file specifying known marker genes for known cell types. |
Nat Commun, 2024 |
INTEGRAL-Radiomics | Radiomics analysis to predict pulmonary nodule malignancy using machine learning approaches | Thorax, 2024 |
R language statistical function package for jointly modelling time-to-event and probability of being event-free. The Firth-type penalized likelihood approach was introduced as an alternative to the MLE approach, to handle heavily censored data with imbalanced categorical covariates | Statistics in Medicine, 2023 | |
Lung Cancer Absolute Risk Models for Mortality in an Asian Population using the China Kadoorie Biobank |
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Astir | Automated inference of cell identity from single-cell multiplexed imaging and proteomics | Cell Systems, 2021 |
JM-SNP |
Characterization of direct and/or indirect genetic associations for multiple traits in longitudinal studies of disease progression with application to diabetes complications |
MedRxiv, 2021 |
TwoPhase_postGWAS |
Two-phase sample selection strategies for design and analysis in post-genome-wide association fine-mapping studies with application to lipids in the Northern Finland Birth Cohort |
Statistics in Medicine, 2021 |
rareBF | Performs region-based testing of rare variants in case-control design | Biometrics, 2021 |
Simulation of genetic variants according to the 1000 Genomes haplotypes |
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Region-based GWAS by Multiple linear combination regression with constraints. Performs genome-wide region-based association testing of common and low-frequency variants with quantitative and binary (case-control) traits, in concert with bigLD/gpart software: human genome partitioning and visualization of high-density SNP data by identifying haplotype blocks. Application to lipids traits in the Canadian Longitudinal Study on Aging |
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genMOSS |
Bayesian Analysis of GWAS data: Performs multi-SNP analysis in the context of GWAS and fine-mapping studies |
Ann Appl Stat., 2016 |
Performs bootstrap bias reduction for effect estimation under the Cox proportional hazards time-to-event model |
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FrailtyPack | General Frailty Models: Shared, Joint and Nested Frailty Models with Prediction- Two functions developed by our group: a) Joint model analysis of recurrent and terminal events in family setting; b) Rare variant analysis in family setting. |