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    58 repositories

    • COMPADRE

      Public
      Pedigree generation software incorporating IBD data from the algorithms behind PRIMUS, ERSA, and PADRE
      pythonbioinformaticsgeneticsperlpopulation-geneticsgenotype-datarelatednessidentity-by-descenthuman-geneticsheredity
      Perl
      •0•0•0•0•Updated Jun 14, 2025Jun 14, 2025

    • drive

      Public
      A cli tool to analyze ibd sharing for a specific locus for multiple phenotypes
      Python
      •
      Apache License 2.0
      •1•0•0•0•Updated Jun 7, 2025Jun 7, 2025

    • compadre-website

      Public
      HTML
      •0•0•0•0•Updated Jun 5, 2025Jun 5, 2025

    • Tractor

      Public
      Scripts for implementing the Tractor pipeline
      Jupyter Notebook
      •
      MIT License
      •10•0•0•0•Updated May 27, 2025May 27, 2025

    • ancQTL

      Public
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated May 16, 2025May 16, 2025

    • hap-ibd

      Public
      The hap-ibd program detects identity-by-descent segments in phased genotype data.
      Java
      •8•0•0•1•Updated May 15, 2025May 15, 2025

    • bioconda-recipes

      Public
      Conda recipes for the bioconda channel.
      Shell
      •
      MIT License
      •3.5k•0•0•0•Updated May 5, 2025May 5, 2025

    • MetaXcan

      Public
      MetaXcan software and manuscript
      Python
      •
      Other
      •97•0•0•1•Updated Apr 29, 2025Apr 29, 2025

    • Concordance-Analysis

      Public
      This analysis was performed to determine if there was concordance between our ancestries-specific GWAS summary statistics. Please see Shaw et al. 2021
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Apr 24, 2025Apr 24, 2025

    • ldsc

      Public
      LD Score Regression (LDSC)
      HTML
      •
      GNU General Public License v3.0
      •355•13•0•0•Updated Dec 16, 2024Dec 16, 2024

    • CCHC_proteomics_QC

      Public
      QC of CCHC proteomics batch2
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Nov 12, 2024Nov 12, 2024

    • unified-simulations

      Public
      Updated simulation code packaged with all of its dependencies.
      Perl
      •0•0•0•0•Updated Nov 1, 2024Nov 1, 2024

    • bioindex-client

      Public
      Gets gene associations from Bioindex
      Python
      •0•0•0•0•Updated Oct 18, 2024Oct 18, 2024

    • rShiny_Bias

      Public
      R
      •1•0•0•0•Updated Sep 19, 2024Sep 19, 2024

    • McBias

      Public
      McBias is an r package designed to help estimate the effects of bias found in large datasets of convenience
      R
      •1•0•0•0•Updated Sep 11, 2024Sep 11, 2024

    • CCHC_lipidomics

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•1•Updated Aug 13, 2024Aug 13, 2024

    • PyVCF3

      Public
      A Variant Call Format reader for Python.
      Python
      •
      Other
      •224•0•0•0•Updated Aug 12, 2024Aug 12, 2024

    • staged-recipes

      Public
      A place to submit conda recipes before they become fully fledged conda-forge feedstocks
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •5.3k•0•0•0•Updated Aug 9, 2024Aug 9, 2024

    • conda-forge-pinning-feedstock

      Public
      A conda-smithy repository for conda-forge-pinning.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •544•0•0•0•Updated Jul 25, 2024Jul 25, 2024

    • docker-builds

      Public
      📦 🐳 Dockerfiles and documentation on tools for public health bioinformatics
      Dockerfile
      •
      GNU General Public License v3.0
      •132•0•0•0•Updated Jul 18, 2024Jul 18, 2024

    • xcftools

      Public
      Set of tools for handling XCF files
      C++
      •3•0•0•0•Updated Jul 18, 2024Jul 18, 2024

    • shapeit5

      Public
      Segmented HAPlotype Estimation and Imputation Tool
      C++
      •
      MIT License
      •13•0•0•0•Updated Jul 18, 2024Jul 18, 2024

    • htslib

      Public
      C library for high-throughput sequencing data formats
      C
      •
      Other
      •452•0•0•0•Updated Jul 9, 2024Jul 9, 2024

    • CCHC_transcriptomics

      Public
      0•0•0•0•Updated May 2, 2024May 2, 2024

    • vcflib

      Public
      C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
      C++
      •
      MIT License
      •223•0•0•0•Updated Apr 29, 2024Apr 29, 2024

    • eQTL_with_GTEx_pipeline

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Apr 22, 2024Apr 22, 2024

    • gargle

      Public
      Infrastructure for calling Google APIs from R, including auth
      R
      •
      Other
      •37•0•0•0•Updated Apr 1, 2024Apr 1, 2024

    • peer

      Public
      A factor analysis package
      C++
      •
      Other
      •43•0•0•1•Updated Mar 28, 2024Mar 28, 2024

    • r-peer

      Public
      A readonly copy of peer packaged as an github_install capable R package
      C++
      •
      Other
      •0•0•0•0•Updated Mar 26, 2024Mar 26, 2024

    • patchwork

      Public
      The Composer of ggplots
      R
      •
      Other
      •165•0•0•0•Updated Mar 25, 2024Mar 25, 2024
    0