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cancerhotspots

Cancer Hotspots

chipimputation

Genotype Imputation Pipeline for H3Africa

docker-ensembl

Dockerfile to build a container with the EnsEMBL Perl API and tools installed

ensembl

The Ensembl Core Perl API and SQL schema

ensembl-funcgen

Ensembl Funcgen Perl API and SQL schema

ensembl-io

File parsing and writing code for Ensembl

ensembl-rest

Language agnostic RESTful data access to Ensembl data over HTTP

ensembl-test

Test libraries and harnesses used for running the Ensembl test suite

ensembl-tools

Ensembl tools including the VEP

ensembl-variation

The Ensembl Variation Perl API and SQL schema

ensembl-vep

The Variant Effect Predictor predicts the functional effects of genomic variants

ensembl-webcode

The code to run an Ensembl website

ensembl-xs

A collection of XS modules to be used with the Ensembl APIs

ensj-healthcheck

Ensembl's Automated QC Framework

hail-on-aws-spot-instances

An option to spin cost effective EMR clusters in AWS with Hail and JupyterNotebook installed

jsonschematomappings

Convert JSON schema to Opensearch / Elasticsearch mappings

loftee

plink-ng

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. Future development will revolve around critical extensions to the core file format (multiallelic variants, dosage, phase).

postgap

Linking GWAS studies to genes through cis-regulatory datasets

public-plugins

Plugins for an Ensembl website

pvac-seq

A cancer immunotherapy pipeline

pytest-mock-resources

Pytest Fixtures that let you actually test against external resource (Postgres, Mongo, Redshift...) dependent code.

vep-lambda

AWS lambda for Ensembl VEP

vep-vcf

Python libraries for parsing VCFs produced by Ensembl VEP

vep_plugins

Plugins for the Ensembl Variant Effect Predictor (VEP)

vepmart

Web interface to search VEP results in elasticsearch index

willcode

Miscellaneous bits of code for my consumption only

windyface