Pinned Repositories
ClinSV
Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data
fast5_fetcher
A tool for fetching nanopore fast5 files after filtering via demultiplexing, alignment, or other, to improve downstream processing efficiency
introme
mity
mity: A highly sensitive mitochondrial variant analysis pipeline for whole genome sequencing data
phenomics-devops
Phenomics code and Jenkins dev-ops setup
rageseq
RAGE-seq scripts
seave
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. Seave is open source and deployable locally, or on a cloud computing provider, and works readily with gene panel, exome and whole genome data, scaling from single labs to multi-institution scale.
seave-databases-annotations
SQL files required to set up the Seave database schema and scripts to import data from annotation sources into the Seave MySQL annotation databases.
seave-documentation
Documentation for how to use and administrate a Seave installation.
vcfscope-measure
Measure the performance of a genomic analysis pipeline
Kinghorn Centre for Clinical Genomics's Repositories
KCCG/ClinSV
Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data
KCCG/mity
mity: A highly sensitive mitochondrial variant analysis pipeline for whole genome sequencing data
KCCG/rageseq
RAGE-seq scripts
KCCG/seave
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. Seave is open source and deployable locally, or on a cloud computing provider, and works readily with gene panel, exome and whole genome data, scaling from single labs to multi-institution scale.
KCCG/introme
KCCG/seave-databases-annotations
SQL files required to set up the Seave database schema and scripts to import data from annotation sources into the Seave MySQL annotation databases.
KCCG/vcfscope-measure
Measure the performance of a genomic analysis pipeline
KCCG/fast5_fetcher
A tool for fetching nanopore fast5 files after filtering via demultiplexing, alignment, or other, to improve downstream processing efficiency
KCCG/homebrew-genomics
Genomics formulae for the Homebrew package manager, brew.sh
KCCG/phenomics-devops
Phenomics code and Jenkins dev-ops setup
KCCG/phenomics-hippo
The Monarch HIPPO: Deriving insight from the medical literature by fuzzy semantic searches over diseases and phenotypes.
KCCG/seave-documentation
Documentation for how to use and administrate a Seave installation.
KCCG/phenomics-affinity
Affinity is a service equipped with Lucene and Luwak for active ontology search hits
KCCG/phenomics-annotation-pipeline
Phenomics annotation and search suite
KCCG/phenomics-notification
KCCG/phenomics-pubmed-ingestion
Amazon Lambda function to fetch, clean and dispatch latest pubmed articles for annotation.
KCCG/phenomics-subscription-worker
A java dcokerized runnable scheduled to perform subscribed searches and send notifications
KCCG/cloudbiolinux
CloudBioLinux: configure virtual (or real) machines with tools for biological analyses
KCCG/genomics-r-intro
Intro to R and RStudio for Genomics
KCCG/kccg-dx-igvserver
IGV server for DNAnexus data
KCCG/POREquality
This is an early version of POREquality, an R Markdown document designed to be ran as part of a Nanopore local basecalling pipeline.
KCCG/refynr
KCCG's cloud-based, genome analysis pipeline
KCCG/shell-genomics
KCCG/TxDb.Hsapiens.UCSC.hg19.ccdsGene
Annotation database generated from UCSC, using CCDS (Consensus CDS IDs)
KCCG/vcfscope-asset
dx Asset bundle, supporting VCFscope
KCCG/vcfscope-reporter
VCFscope report generation app.
KCCG/wrangling-genomics