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    35 repositories

    • phaser_tuneup

      Public
      Tuning up phaser without major modifications in logic and algorithms
      Python
      •
      GNU General Public License v3.0
      •36•0•0•1•Updated Aug 25, 2026Aug 25, 2026

    • Pantry

      Public
      Pan-transcriptomic phenotyping
      rna-seqgeneticstranscriptomics
      rna-seqgeneticstranscriptomics
      Python
      •
      MIT License
      •0•20•2•0•Updated Aug 24, 2026Aug 24, 2026

    • fusion_twas_tuneup

      Public
      bye identifcal tune up of fusion_twas from gusevlab by PejLab
      R
      •
      GNU General Public License v3.0
      •50•0•0•0•Updated Jun 26, 2026Jun 26, 2026

    • pejlab.github.io

      Public
      Website for the PejLab
      SCSS
      •
      MIT License
      •0•0•0•0•Updated May 13, 2026May 13, 2026

    • LaDDR

      Public
      Extract latent transcriptomic phenotypes
      Python
      •
      MIT License
      •0•1•2•0•Updated Apr 29, 2026Apr 29, 2026

    • .github

      Public
      Genomic Data Modeling Lab at Seattle Children's and the University of Washington
      0•0•0•0•Updated Apr 6, 2026Apr 6, 2026

    • ANEVAh_repo

      Public
      Repository for ANEVA-h
      R
      •
      Other
      •0•0•0•0•Updated Apr 16, 2025Apr 16, 2025

    • Contaminated_ASE

      Public
      Synthetically Contaminated ASE Data used for Benchmarking ASEQC
      0•0•0•0•Updated Apr 16, 2025Apr 16, 2025

    • ASE_FP_Lists

      Public
      False positive prone genes for GTEx v8 ASE Data
      0•0•0•0•Updated Apr 15, 2025Apr 15, 2025

    • ASE_Data

      Public
      Allele-Specifc Expression Data From Reference Cohorts
      0•0•0•0•Updated Apr 15, 2025Apr 15, 2025

    • ASE_VG

      Public
      Reference VG Statistics from Reference Datasets using Haplotype-level ANEVA
      0•0•0•0•Updated Apr 15, 2025Apr 15, 2025

    • aseQC_repo

      Public
      Allele Specific Expression Quality Control Pipeline
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Apr 14, 2025Apr 14, 2025

    • ASE_Cases

      Public
      Gene-level Allele Specific Expression Data from Case Cohorts
      0•0•0•0•Updated Apr 11, 2025Apr 11, 2025

    • blnm

      Public
      Tools for sampling and parameter inference of the binomial-logit-normal distribution.
      Python
      •
      Apache License 2.0
      •2•0•2•3•Updated Apr 5, 2025Apr 5, 2025

    • aFCn

      Public
      Cython
      •
      Apache License 2.0
      •2•2•1•2•Updated Dec 5, 2024Dec 5, 2024

    • haptwas

      Public
      Haplotype Aware TWAS project
      Python
      •
      Apache License 2.0
      •1•0•3•0•Updated Oct 10, 2024Oct 10, 2024

    • gene_expr_pred

      Public
      Python
      •
      Apache License 2.0
      •2•1•2•0•Updated Aug 15, 2024Aug 15, 2024

    • aFCs

      Public
      Contains GTEX aFC estimates
      Jupyter Notebook
      •0•1•0•0•Updated Oct 16, 2023Oct 16, 2023

    • bln

      Public
      An R implementation of the Binomial-Logit-Normal distribution
      R
      •
      Apache License 2.0
      •1•1•1•0•Updated Jul 18, 2022Jul 18, 2022

    • ANEVA-DOT

      Public
      Tests Allelic Expression data for extreme imbalance w.r.t. population
      R
      •
      Apache License 2.0
      •8•11•4•2•Updated Oct 8, 2021Oct 8, 2021

    • ANEVA-DOT_reference_datasets

      Public
      ANEVA-DOT reference datasets
      Jupyter Notebook
      •2•0•0•0•Updated Nov 17, 2020Nov 17, 2020

    • Datasets

      Public
      Our old repo for storing our datasets
      0•0•0•0•Updated Oct 17, 2020Oct 17, 2020

    • ANEVA

      Public
      ANalysis of Expression VAriance
      MATLAB
      •
      Apache License 2.0
      •1•4•1•0•Updated May 28, 2020May 28, 2020

    • gtex-pipeline

      Public
      GTEx & TOPMed data production and analysis pipelines
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •186•0•0•0•Updated Mar 27, 2020Mar 27, 2020

    • jupyter-slack-notify

      Public
      A magic command for notifications via slack
      Python
      •
      MIT License
      •13•0•0•0•Updated Dec 11, 2019Dec 11, 2019

    • vgdat

      Public
      Utilities and starter code to match Ensembl IDs with population variance estimates from GTEx v7.
      R
      •0•0•0•0•Updated May 10, 2019May 10, 2019

    • phaser

      Public
      phasing and Allele Specific Expression from RNA-seq
      Python
      •
      GNU General Public License v3.0
      •36•0•0•0•Updated Mar 23, 2019Mar 23, 2019

    • TiMEx

      Public
      Bioconductor package for finding mutually exclusive groups of alterations in large cancer datasets
      R
      •3•0•0•0•Updated Nov 12, 2018Nov 12, 2018

    • allelecounter

      Public
      Counts the number of reads which map to either the reference or alternate allele at each heterozygous SNP.
      Python
      •9•0•0•0•Updated Sep 21, 2018Sep 21, 2018

    • aFC

      Public
      Calculates allelic Fold Change (aFC) using standard input files for fastQTL.
      Python
      •11•0•0•0•Updated Sep 19, 2018Sep 19, 2018
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