Discover Ensembl/ensembl-biomart Open Source project

Basic operations on the space of numerical functions defined on the genome using lazy evaluators for flexibility and efficiency

394

WiggleTools

142

ensembl-rest

Language agnostic RESTful data access to Ensembl data over HTTP

Plugins for the Ensembl Variant Effect Predictor (VEP)

128

VEP_plugins

The Ensembl Core Perl API and SQL schema

113

ensembl

*DEPRECATED* Job management for the Ensembl Genebuild pipeline

ensembl-pipeline

EnsEMBL Hive - a system for creating and running pipelines on a distributed compute resource

ensembl-hive

The Ensembl Compara Perl API and SQL schema

ensembl-compara

Linking GWAS studies to genes through cis-regulatory datasets

postgap

Jupyter Notebook

plant-scripts

Scripting analyses of genomes in Ensembl Plants

ensembl-tools

Ensembl tools

The Ensembl Variation Perl API and SQL schema

ensembl-variation

Git repo for Bio::DB::HTS module on CPAN, providing Perl links into HTSlib

Bio-DB-HTS

The code to run an Ensembl website

ensembl-webcode

Ensembl Funcgen Perl API and SQL schema

ensembl-funcgen

Modules to interface with tools used in Ensembl Gene Annotation Process and scripts to run pipelines

ensembl-analysis

Ensembl's Automated QC Framework

ensembl-client

Ensembl beta client

TypeScript

ensj-healthcheck

Java

ensembl-production

Ensembl Production code

ensembl-anno

A collection of tools which Ensembl uses to work with Git

ensembl-git-tools

Plugins for an Ensembl website

public-plugins

HTML

ensembl-io

File parsing and writing code for Ensembl

Pipelines to turn basic genomic data into Ensembl cores and back

ensembl-genomio

This folder contains scripts to access/use the TreeFam database

treefam_tools

Takes RelaxNG schema as input and generates corresponding code for a Blockly block to represent the same

XML-To-Blockly

homebrew-ensembl

Core formula for Ensembl

Specifications and implementation of the TrackHub registry

trackhub-registry

Tools and documentation for Plants

plant_tools

EpiRR

A registry of epigenomics reference data sets

ols-client

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

ensembl-xs

Test libraries and harnesses used for running the Ensembl test suite

ensembl-test

Code for checking Ensembl databases during release production

ensembl-datacheck

A eHive Pipeline for loading Ensembl and Ensembl Genomes databases to a MySQL compatible server

ensembl-database-loader

Python and R notebooks to be used by Jupyter

rest-api-jupyter-course

Jupyter Notebook

ensembl-metadata

API for storing and querying metadata from Ensembl and EnsemblGenomes

Graphical interface for the eHive workflow manager

guiHive

Python Ensembl code source repository

ensembl-py

ensembl-web-docker

tark

homebrew-external

Formulas hosted from the homebrew project from retired or third party repos with minor edits

Python Ensembl Gene Annotation code source repository

ensembl-genes

C API for the Ensembl Database

ensc-core

GIFTS

Tools for automatic server deployment

ensembl-rest-deploy

Meta formulas for homebrew/linuxbrew

homebrew-cask

Archive documentation of the Ensembl infrastructure. Information here is probably out of date.

ensembl-doc

TeX

ensembl-utils

Ensembl python utils

Presentations used in Ensembl workshops

ensembl-presentation

Transformer model for gene symbol assignment of protein coding sequences

gene_symbol_transformer

ensembl-otter

'PBS Pro' implementation of Ensembl Hive Meadow interface

ensembl-hive-pbspro

The Ensembl gene annotation pipeline (a work in progress)

ensembl-annotation

A collection of formulas where the source/archive is not readily available from a public URL

homebrew-moonshine

Ensembl production service portal

ensembl-production-services

gsoc-dl-protein-coding-genes

Ensembl 2020 server backend

ensembl-2020-server

Perl XS bindings to libBigWig for access the UCSC/kent big formats

Bio-DB-Big

REST API for ensembl-metadata

ensembl-metadata-registry

Code for NextFlow pipeline to find and annotate repeats (GSoC project)

repeat_nf

Nextflow

ensembl-datacheck-py

Wrapper for the storage of large numerical arrays

ensembl-glossary

Makefile

ensembl-hdf5

cwl-udocker-tests

A repository for testing udocker, cwl and toil

Shell

ensembl-2020-genome-search

Genome search backend microservice for ensembl 2020

A collection of homebrew formula for working with ICC and ICCMPI programs

homebrew-icc

gene_pcp

Genebuild project - classifying protein-coding potential via a machine learning approach

A collection of additional cpanfiles that have no natural home with any project

cpanfiles

Sets of requirements files required to install a tool or setup a virtualenv

python-requirements

gti-genesearch

Query manager and REST interface to Advanced Search

Java

webvm

Son of Ariadne, a GraphQL server and supporting software

ensembl-thoas

Modified version of pantherScore that is used to classify proteins in the Ensembl Compara / TreeFam pipeline

pantherScore

treefam-webcode

Web-code for the TreeFam website

Metazoan production helper library and script to import ad-hoc annotations.

ensembl-production-metazoa

Shell

Finemap

Service for downloading and consuming external data

VersioningService

API for accessing NCBI taxonomy

ensembl-taxonomy

HTCondor Meadow for Ensembl Hive

ensembl-hive-htcondor

ensembl-prodinf-djcore

ensembl-prodinf-datachecks

ensembl-prodinf-tools

Schema for the Ensembl ontology database

ensembl-ontology-schema

TSQL

ensembl-2020-static-assests

Static assets for new site

ensembl-git-test

Dummy repository to test git operations and scripts

ensembl-prodinf-legacy-core

Django app template files

ensembl-dj-app

fuse8

fuse8 for ensembl

gifts_rest

Template to be reused when using django-admin startproject command

ensembl-dj-project

Second implementation of Trackhub Registry

thr

PerlModules

ensembl-genome-browser

Ensembl genome browser

ensembl-killlist

Web app for accessing Ensembl Production services

ensembl-prodinf-web

*DEPRECATED* Code to load external data in the Ensembl website

gene_finder

Jupyter Notebook

ensembl-external