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    27 repositories

    • ClinSV

      Public
      Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data
      structural-variation
      Perl
      •
      Other
      •8•65•18•0•Updated Sep 4, 2024Sep 4, 2024

    • mity

      Public
      mity: A highly sensitive mitochondrial variant analysis pipeline for whole genome sequencing data
      bioinformaticsgenomicswhole-genome-sequencingprecision-medicinemitochondria
      Python
      •
      MIT License
      •4•36•4•0•Updated Jun 7, 2024Jun 7, 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•17•3•0•Updated Aug 30, 2021Aug 30, 2021

    • genomics-r-intro

      Public
      Intro to R and RStudio for Genomics
      Python
      •
      Other
      •89•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
      •188•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
      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 popular disease databases. Seave stores genomic variation of all types and sizes, and allows filtering for specific inheritance patterns, quality values, allele frequencies and gene lists. …
      htmlphpbioinformaticsresearchwebgenomicsgeneticssequencingclinicalgemini
      HTML
      •
      Other
      •3•15•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
      •158•0•0•0•Updated Jul 23, 2014Jul 23, 2014