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    55 repositories

    • YCSGP.github.io

      Public
      HTML
      •
      MIT License
      •2•2•0•0•Updated Aug 27, 2025Aug 27, 2025

    • JointPRS

      Public
      Python
      •
      MIT License
      •1•0•0•0•Updated Aug 16, 2025Aug 16, 2025

    • EEPRS

      Public
      1•0•0•0•Updated Jul 24, 2025Jul 24, 2025

    • MIXPRS

      Public
      Python
      •1•0•0•0•Updated Jul 1, 2025Jul 1, 2025

    • scMODAL

      Public
      scMODAL: A general deep learning framework for single-cell Multi-Omics Data Alignment with feature Links
      Python
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated Jun 10, 2025Jun 10, 2025

    • PERADIGM

      Public
      PERADIGM: Phenotype Embedding Similarity-based Rare Disease Gene Mapping
      R
      •1•0•0•0•Updated Apr 24, 2025Apr 24, 2025

    • Pathway-Analysis-using-Random-Forest

      Public
      An R code for pathway-based classification and regression using Random Forests.
      0•0•0•0•Updated Mar 3, 2025Mar 3, 2025

    • LORS

      Public
      A Low-Rank representation and Sparse regression for eQTL mapping. This algorithm accounts for confounding factors such as unobserved covariates, experimental artifacts, and unknown environmental perturbations.
      MATLAB
      •0•0•0•0•Updated Mar 3, 2025Mar 3, 2025

    • GWAS-with-MRF-pathway

      Public
      This is a program to implement the Markov Random Field (MRF) method to incorporate pathway topology for genome wide association studies.
      R
      •0•0•0•0•Updated Mar 3, 2025Mar 3, 2025

    • viRandomForests

      Public
      Variable importance-weighted Random Forests (viRandomForests) is an R package, which samples features according to their variable importance scores, and then selects the best split from the randomly selected features, to improved prediction accuracy in the presence of weak signals and large noises.
      0•0•0•0•Updated Mar 2, 2025Mar 2, 2025

    • GWAS.PC

      Public
      GWAS.PC (GWAS Power Calculation) is an R package that does power analysis in genome wide association studies. In particular, genotyping error is considered in power calculation.
      R
      •0•0•0•0•Updated Mar 2, 2025Mar 2, 2025

    • gbr

      Public
      This is an R package implementing a post-GWAS prioritization algorithm, which incorporates the rewiring information of co-expression network to prioritize GWAS signals.
      R
      •0•0•0•0•Updated Mar 2, 2025Mar 2, 2025

    • COSINE

      Public
      ❗ This is a read-only mirror of the CRAN R package repository. COSINE — COndition SpecIfic sub-NEtwork
      R
      •2•0•0•0•Updated Mar 2, 2025Mar 2, 2025

    • UTMOST

      Public
      UTMOST (unified test for molecular signatures) is a method for cross-tissue gene expression imputation for transcriptome-wide association analyses.
      Python
      •19•0•0•0•Updated Mar 2, 2025Mar 2, 2025

    • GenomeAnnotation

      Public
      0•0•0•0•Updated Mar 1, 2025Mar 1, 2025

    • SDPRX

      Public
      A statistical method for cross-population prediction of complex traits
      Python
      •
      MIT License
      •1•0•0•0•Updated Feb 21, 2025Feb 21, 2025

    • TWASKnockoff

      Public
      TWASKnockoff: A Knockoff-based Framework for Causal Genes Identifications
      R
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated Feb 10, 2025Feb 10, 2025

    • SuSiE2

      Public
      Code for simulations and real data analysis for SuSiE2
      R
      •1•0•0•0•Updated Jan 17, 2025Jan 17, 2025

    • CosGeneGate

      Public
      Python
      •
      MIT License
      •2•0•0•0•Updated Jan 17, 2025Jan 17, 2025

    • scLAMBDA

      Public
      Modeling and predicting single-cell multi-gene perturbation responses with scLAMBDA
      Python
      •
      GNU General Public License v3.0
      •6•0•0•0•Updated Jan 14, 2025Jan 14, 2025

    • CASE

      Public
      CASE: Cell-type-specific And Shared EQTL Fine-mapping
      R
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated Dec 15, 2024Dec 15, 2024

    • SpacePAC

      Public
      This is a read-only mirror of the git repos at https://bioconductor.org
      TeX
      •1•0•0•0•Updated Dec 8, 2024Dec 8, 2024

    • QuartPAC

      Public
      This is a read-only mirror of the git repos at https://bioconductor.org
      TeX
      •1•0•0•0•Updated Dec 8, 2024Dec 8, 2024

    • dcGSA

      Public
      This is a read-only mirror of the git repos at https://bioconductor.org
      R
      •1•0•0•0•Updated Dec 7, 2024Dec 7, 2024

    • MARBLES

      Public
      A Markov Random Field Model-Based Approach for Differentially Expressed Gene Detection in Single-cell RNA-seq Data
      R
      •1•0•0•0•Updated Dec 4, 2024Dec 4, 2024

    • LDER-GE

      Public
      We propose a statistical method to estimate the phenotypic variance explained by Gene-Envieonment interactions. The method is called Linkage-Disequilibrium Eigenvalue Regression for Gene-Environment interactions (LDER-GE).
      R
      •
      MIT License
      •7•0•0•0•Updated Nov 26, 2024Nov 26, 2024

    • SDPR_admix

      Public
      A statistical method to calculate PRS in admixed population
      C
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated Nov 26, 2024Nov 26, 2024

    • SDPR

      Public
      A fast and robust Bayesian nonparametric method for prediction of complex traits using GWAS summary statistics
      C
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated Nov 18, 2024Nov 18, 2024

    • SplitClusterTest.jl

      Public
      Julia package for "FDR Control via Data Splitting for Testing-after-Clustering (arXiv: 2410.06451)"
      Julia
      •
      MIT License
      •1•0•0•0•Updated Nov 6, 2024Nov 6, 2024

    • SplitClusterTest

      Public
      R package for "FDR Control via Data Splitting for Testing-after-Clustering (arXiv: 2410.06451)"
      R
      •
      Other
      •2•0•0•0•Updated Nov 6, 2024Nov 6, 2024