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    17 repositories

    • RVMMAT

      Public
      R package that performs retrospective varying coefficients mixed model association test for longitudinal binary traits in population samples.
      R
      •0•0•0•0•Updated Sep 22, 2024Sep 22, 2024

    • DML-RC

      Public
      DML-RC is a double/debiased machine learning approach with regression calibration to correct for bias due to measurement error. This approach is designed for evaluating the causal effects of correlated multi-pollutant PM2.5 constituents measured with correlated error.
      Python
      •
      MIT License
      •0•1•0•0•Updated Sep 20, 2024Sep 20, 2024

    • DML-RC_simulations

      Public
      DML-RC_simulations contains all files to replicate the simulation study in the DML-RC paper.
      R
      •
      MIT License
      •0•0•0•0•Updated Sep 19, 2024Sep 19, 2024

    • MAGEIT2

      Public
      Marginal Gene-Environment Interaction Test with RANdom or FIXed
      C++
      •0•0•0•0•Updated Sep 17, 2024Sep 17, 2024

    • tRFtarget-pipeline

      Public
      tRFtarget-pipeline is designed to find RNA-RNA interaction sites between transfer RNA-derived fragments (tRFs) and target RNAs, and is used in tRFtarget database (http://trftarget.net/).
      Python
      •
      MIT License
      •0•1•0•0•Updated Jul 22, 2024Jul 22, 2024

    • tRFtarget

      Public
      tRFtarget (http://trftarget.net/) is a comprehensive platform consolidating both computationally predicted and experimentally validated binding interactions between transfer RNA-derived fragments (tRFs) and target transcripts across multiple organisms.
      JavaScript
      •
      MIT License
      •1•2•12•0•Updated Jun 8, 2023Jun 8, 2023

    • SDePER_Analysis

      Public
      This Github repository holds Notebooks and results of running SDePER on both Simulated and Real datasets, and Notebooks for Figure Panels in manuscript.
      HTML
      •
      MIT License
      •2•0•0•0•Updated May 2, 2023May 2, 2023

    • SDePER

      Public
      SDePER is a two-step hybrid machine learning and regression method considering platform effect, spatial information and sparsity in deconvolution of spatial transcriptomic data using reference single-cell RNA sequencing data. It's also able to impute cell type compositions and gene expression at enhanced resolution.
      Python
      •
      MIT License
      •1•0•0•0•Updated May 1, 2023May 1, 2023

    • RSIT

      Public
      R package that performs retrospective set-based gene-environment interaction tests for binary traits.
      R
      •0•0•0•0•Updated Feb 3, 2023Feb 3, 2023

    • iDESC

      Public
      iDESC package for DE analysis in scRNA-seq data
      R
      •
      Other
      •2•0•0•0•Updated Jul 28, 2022Jul 28, 2022

    • RSVMMAT

      Public
      R package that performs retrospective set-based varying coefficient mixed model association tests for longitudinal binary traits.
      R
      •0•0•0•0•Updated Apr 18, 2022Apr 18, 2022

    • G2S3_paper2020

      Public
      R
      •1•0•0•0•Updated May 14, 2021May 14, 2021

    • G2S3

      Public
      G2S3 (Sparse and Smooth Signal of Gene Graph-based imputation)
      scrna-seqgraphsignalprocessingscrna-imputation-methods
      MATLAB
      •
      GNU General Public License v3.0
      •0•3•0•0•Updated May 14, 2021May 14, 2021

    • LBRAT

      Public
      R package for retrospective association testing for longitudinal binary traits
      gwasgeneticsretrospective-association-analysislongitudinal-binary-traits
      R
      •
      MIT License
      •1•4•0•0•Updated Mar 5, 2020Mar 5, 2020

    • LSRAT

      Public
      R package for retrospective variant-set testing for longitudinal traits in genome-wide association studies
      gwaslongitudinal-dataassociation-analysisgene-level
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Mar 5, 2020Mar 5, 2020

    • fGWAS

      Public
      GWAS tools for longitudinal genetic traits based on fGWAS statistical model
      gwasrgeneticsfgwaslongitudinal
      R
      •0•1•0•0•Updated Oct 24, 2018Oct 24, 2018

    • LSKAT

      Public
      C++
      •1•1•0•1•Updated Oct 23, 2017Oct 23, 2017