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    27 repositories

    • mity

      Public
      mity: A highly sensitive mitochondrial variant analysis pipeline for whole genome sequencing data
      bioinformaticsgenomicswhole-genome-sequencing
      bioinformaticsgenomicswhole-genome-sequencingprecision-medicinemitochondria
      Python
      •
      MIT License
      •7•40•5•0•Updated Sep 8, 2025Sep 8, 2025

    • ClinSV

      Public
      Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data
      structural-variation
      structural-variation
      Perl
      •
      Other
      •8•75•24•0•Updated Sep 4, 2024Sep 4, 2024

    • phenomics-devops

      Public
      Phenomics code and Jenkins dev-ops setup
      Python
      •
      GNU General Public License v3.0
      •0•1•0•4•Updated Dec 8, 2022Dec 8, 2022

    • rageseq

      Public
      RAGE-seq scripts
      Perl
      •3•18•3•0•Updated Aug 30, 2021Aug 30, 2021

    • genomics-r-intro

      Public
      Intro to R and RStudio for Genomics
      Python
      •
      Other
      •92•0•0•0•Updated Apr 23, 2021Apr 23, 2021

    • wrangling-genomics

      Public
      Python
      •
      Other
      •151•0•0•0•Updated Mar 19, 2021Mar 19, 2021

    • shell-genomics

      Public
      Python
      •
      Other
      •197•0•0•0•Updated Mar 12, 2021Mar 12, 2021

    • fast5_fetcher

      Public
      A tool for fetching nanopore fast5 files after filtering via demultiplexing, alignment, or other, to improve downstream processing efficiency
      Python
      •
      MIT License
      •4•1•0•1•Updated Feb 13, 2019Feb 13, 2019

    • phenomics-subscription-worker

      Public
      A java dcokerized runnable scheduled to perform subscribed searches and send notifications
      Java
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Oct 5, 2018Oct 5, 2018

    • phenomics-notification

      Public
      Java
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Oct 5, 2018Oct 5, 2018

    • phenomics-pubmed-ingestion

      Public
      Amazon Lambda function to fetch, clean and dispatch latest pubmed articles for annotation.
      Java
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Oct 5, 2018Oct 5, 2018

    • phenomics-affinity

      Public
      Affinity is a service equipped with Lucene and Luwak for active ontology search hits
      Java
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Oct 5, 2018Oct 5, 2018

    • phenomics-hippo

      Public
      The Monarch HIPPO: Deriving insight from the medical literature by fuzzy semantic searches over diseases and phenotypes.
      JavaScript
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Oct 5, 2018Oct 5, 2018

    • phenomics-annotation-pipeline

      Public
      Phenomics annotation and search suite
      Java
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Oct 5, 2018Oct 5, 2018

    • vcfscope-asset

      Public
      dx Asset bundle, supporting VCFscope
      Makefile
      •
      GNU General Public License v3.0
      •2•0•0•1•Updated Sep 20, 2018Sep 20, 2018

    • introme

      Public
      bioinformatics
      bioinformatics
      Shell
      •0•6•0•0•Updated Aug 10, 2018Aug 10, 2018

    • seave

      Public
      Seave is a web platform that enables genetic variants to be easily filtered and annotated with in silico pathogenicity prediction scores and annotations from po…
      htmlphpbioinformatics
      htmlphpbioinformaticsresearchwebgenomicsgeneticssequencingclinicalgemini
      HTML
      •
      Other
      •3•16•0•0•Updated Aug 9, 2018Aug 9, 2018

    • vcfscope-measure

      Public
      Measure the performance of a genomic analysis pipeline
      Perl
      •
      GNU General Public License v3.0
      •2•2•0•1•Updated Aug 7, 2018Aug 7, 2018

    • POREquality

      Public
      This is an early version of POREquality, an R Markdown document designed to be ran as part of a Nanopore local basecalling pipeline.
      MIT License
      •7•0•0•0•Updated Jul 16, 2018Jul 16, 2018

    • seave-documentation

      Public
      Documentation for how to use and administrate a Seave installation.
      TeX
      •0•1•0•0•Updated May 7, 2018May 7, 2018

    • seave-databases-annotations

      Public
      SQL files required to set up the Seave database schema and scripts to import data from annotation sources into the Seave MySQL annotation databases.
      Perl
      •
      Other
      •2•2•0•0•Updated Mar 23, 2018Mar 23, 2018

    • refynr

      Public
      KCCG's cloud-based, genome analysis pipeline
      1•0•0•0•Updated Dec 1, 2017Dec 1, 2017

    • kccg-dx-igvserver

      Public
      IGV server for DNAnexus data
      Python
      •0•0•0•0•Updated Sep 26, 2017Sep 26, 2017

    • vcfscope-reporter

      Public
      VCFscope report generation app.
      R
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Feb 28, 2017Feb 28, 2017

    • TxDb.Hsapiens.UCSC.hg19.ccdsGene

      Public
      Annotation database generated from UCSC, using CCDS (Consensus CDS IDs)
      R
      •0•0•0•0•Updated Jan 31, 2017Jan 31, 2017

    • homebrew-genomics

      Public
      Genomics formulae for the Homebrew package manager, brew.sh
      Ruby
      •
      Other
      •0•1•0•0•Updated Jan 19, 2017Jan 19, 2017

    • cloudbiolinux

      Public
      CloudBioLinux: configure virtual (or real) machines with tools for biological analyses
      Python
      •
      MIT License
      •155•0•0•0•Updated Jul 23, 2014Jul 23, 2014