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    56 repositories

    • 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 Nov 13, 2024Nov 13, 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

    • compadre

      Public
      IBD-based pedigree generation software, built on top of and maximizing utility from the tools PRIMUS and ERSA
      pythonbioinformaticsbig-datageneticsperlpopulation-geneticsrelatednessidentity-by-descenthuman-geneticspedigrees
      Perl
      •0•0•1•1•Updated Oct 22, 2024Oct 22, 2024

    • bioindex-client

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

    • ldsc

      Public
      LD Score Regression (LDSC)
      HTML
      •
      GNU General Public License v3.0
      •344•9•0•0•Updated Oct 7, 2024Oct 7, 2024

    • compadre-website

      Public
      HTML
      •0•0•0•0•Updated Oct 1, 2024Oct 1, 2024

    • rShiny_Bias

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

    • hap-ibd

      Public
      The hap-ibd program detects identity-by-descent segments in phased genotype data.
      Java
      •8•0•0•0•Updated Sep 16, 2024Sep 16, 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
      •5k•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
      •500•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
      •124•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
      •11•0•0•0•Updated Jul 18, 2024Jul 18, 2024

    • htslib

      Public
      C library for high-throughput sequencing data formats
      C
      •
      Other
      •447•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
      •221•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
      •33•0•0•0•Updated Apr 1, 2024Apr 1, 2024

    • peer

      Public
      A factor analysis package
      C++
      •
      Other
      •41•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
      •163•0•0•0•Updated Mar 25, 2024Mar 25, 2024

    • MetaXcan

      Public
      MetaXcan software and manuscript
      Python
      •
      Other
      •92•0•0•1•Updated Mar 10, 2024Mar 10, 2024

    • phaser

      Public
      phasing and Allele Specific Expression from RNA-seq
      Python
      •
      GNU General Public License v3.0
      •36•0•0•0•Updated Mar 8, 2024Mar 8, 2024

    • plink-ng

      Public
      A comprehensive update to the PLINK association analysis toolset. Beta testing of the first new version (1.90), focused on speed and memory efficiency improvements, is finishing up. Development is now focused on building out support for multiallelic, phased, and dosage data in PLINK 2.0.
      C
      •126•0•0•0•Updated Feb 29, 2024Feb 29, 2024

    • SAIGE-1

      Public
      Development for SAIGE and SAIGE-GENE(+)
      C++
      •
      GNU General Public License v3.0
      •29•0•0•0•Updated Feb 26, 2024Feb 26, 2024

    • snakemake-wrappers

      Public
      This is the development home of the Snakemake wrapper repository, see
      Python
      •186•0•0•0•Updated Feb 23, 2024Feb 23, 2024