Ensembl Project (@Ensembl)
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Top repositories

1

ensembl-vep

The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
Perl
394
star
2

WiggleTools

Basic operations on the space of numerical functions defined on the genome using lazy evaluators for flexibility and efficiency
C
142
star
3

ensembl-rest

Language agnostic RESTful data access to Ensembl data over HTTP
Perl
128
star
4

VEP_plugins

Plugins for the Ensembl Variant Effect Predictor (VEP)
Perl
113
star
5

ensembl

The Ensembl Core Perl API and SQL schema
Perl
74
star
6

ensembl-pipeline

*DEPRECATED* Job management for the Ensembl Genebuild pipeline
Perl
59
star
7

ensembl-hive

EnsEMBL Hive - a system for creating and running pipelines on a distributed compute resource
Perl
49
star
8

ensembl-compara

The Ensembl Compara Perl API and SQL schema
Perl
45
star
9

postgap

Linking GWAS studies to genes through cis-regulatory datasets
Jupyter Notebook
38
star
10

plant-scripts

Scripting analyses of genomes in Ensembl Plants
Perl
36
star
11

ensembl-tools

Ensembl tools
Perl
32
star
12

ensembl-variation

The Ensembl Variation Perl API and SQL schema
Perl
26
star
13

Bio-DB-HTS

Git repo for Bio::DB::HTS module on CPAN, providing Perl links into HTSlib
Perl
24
star
14

ensembl-webcode

The code to run an Ensembl website
Perl
21
star
15

ensembl-funcgen

Ensembl Funcgen Perl API and SQL schema
Perl
14
star
16

ensembl-analysis

Modules to interface with tools used in Ensembl Gene Annotation Process and scripts to run pipelines
Perl
13
star
17

ensembl-client

Ensembl beta client
TypeScript
12
star
18

ensj-healthcheck

Ensembl's Automated QC Framework
Java
10
star
19

ensembl-production

Ensembl Production code
Perl
10
star
20

ensembl-anno

Python
9
star
21

ensembl-git-tools

A collection of tools which Ensembl uses to work with Git
Perl
9
star
22

public-plugins

Plugins for an Ensembl website
HTML
9
star
23

ensembl-io

File parsing and writing code for Ensembl
Perl
9
star
24

ensembl-genomio

Pipelines to turn basic genomic data into Ensembl cores and back
Python
9
star
25

treefam_tools

This folder contains scripts to access/use the TreeFam database
Perl
8
star
26

XML-To-Blockly

Takes RelaxNG schema as input and generates corresponding code for a Blockly block to represent the same
JavaScript
8
star
27

homebrew-ensembl

Core formula for Ensembl
Ruby
8
star
28

trackhub-registry

Specifications and implementation of the TrackHub registry
Perl
7
star
29

plant_tools

Tools and documentation for Plants
M
7
star
30

EpiRR

A registry of epigenomics reference data sets
Perl
6
star
31

ols-client

Python
6
star
32

ensembl-xs

A collection of XS modules to be used with the Ensembl APIs
Perl
6
star
33

ensembl-test

Test libraries and harnesses used for running the Ensembl test suite
Perl
6
star
34

ensembl-datacheck

Code for checking Ensembl databases during release production
Perl
5
star
35

ensembl-database-loader

A eHive Pipeline for loading Ensembl and Ensembl Genomes databases to a MySQL compatible server
Perl
5
star
36

rest-api-jupyter-course

Python and R notebooks to be used by Jupyter
Jupyter Notebook
5
star
37

ensembl-metadata

API for storing and querying metadata from Ensembl and EnsemblGenomes
Perl
5
star
38

guiHive

Graphical interface for the eHive workflow manager
JavaScript
5
star
39

ensembl-py

Python Ensembl code source repository
Python
5
star
40

ensembl-web-docker

ensembl-web docker
HTML
4
star
41

tark

HTML
4
star
42

homebrew-external

Formulas hosted from the homebrew project from retired or third party repos with minor edits
Ruby
4
star
43

ensembl-genes

Python Ensembl Gene Annotation code source repository
Python
4
star
44

ensc-core

C API for the Ensembl Database
C
3
star
45

GIFTS

Perl
3
star
46

ensembl-biomart

Code to build the ensembl and ensembl genomes marts
Perl
3
star
47

ensembl-rest-deploy

Tools for automatic server deployment
Ruby
3
star
48

homebrew-cask

Meta formulas for homebrew/linuxbrew
Ruby
3
star
49

ensembl-doc

Archive documentation of the Ensembl infrastructure. Information here is probably out of date.
TeX
3
star
50

ensembl-utils

Ensembl python utils
Python
3
star
51

ensembl-presentation

Presentations used in Ensembl workshops
Perl
3
star
52

gene_symbol_transformer

Transformer model for gene symbol assignment of protein coding sequences
Python
3
star
53

ensembl-otter

Perl
3
star
54

ensembl-hive-pbspro

'PBS Pro' implementation of Ensembl Hive Meadow interface
Perl
3
star
55

ensembl-annotation

The Ensembl gene annotation pipeline (a work in progress)
Perl
2
star
56

homebrew-moonshine

A collection of formulas where the source/archive is not readily available from a public URL
Ruby
2
star
57

ensembl-production-services

Ensembl production service portal
Python
2
star
58

gsoc-dl-protein-coding-genes

Python
2
star
59

ensembl-2020-server

Ensembl 2020 server backend
Python
2
star
60

Bio-DB-Big

Perl XS bindings to libBigWig for access the UCSC/kent big formats
Perl
2
star
61

ensembl-metadata-registry

REST API for ensembl-metadata
Python
2
star
62

repeat_nf

Code for NextFlow pipeline to find and annotate repeats (GSoC project)
Nextflow
2
star
63

ensembl-datacheck-py

Python
2
star
64

ensembl-glossary

Makefile
2
star
65

ensembl-hdf5

Wrapper for the storage of large numerical arrays
C
2
star
66

cwl-udocker-tests

A repository for testing udocker, cwl and toil
Shell
2
star
67

ensembl-2020-genome-search

Genome search backend microservice for ensembl 2020
Python
2
star
68

homebrew-icc

A collection of homebrew formula for working with ICC and ICCMPI programs
2
star
69

gene_pcp

Genebuild project - classifying protein-coding potential via a machine learning approach
Python
2
star
70

cpanfiles

A collection of additional cpanfiles that have no natural home with any project
Perl
2
star
71

python-requirements

Sets of requirements files required to install a tool or setup a virtualenv
2
star
72

gti-genesearch

Query manager and REST interface to Advanced Search
Java
2
star
73

webvm

Perl
2
star
74

ensembl-thoas

Son of Ariadne, a GraphQL server and supporting software
Python
2
star
75

pantherScore

Modified version of pantherScore that is used to classify proteins in the Ensembl Compara / TreeFam pipeline
2
star
76

treefam-webcode

Web-code for the TreeFam website
JavaScript
2
star
77

ensembl-production-metazoa

Metazoan production helper library and script to import ad-hoc annotations.
Shell
1
star
78

Finemap

Python
1
star
79

VersioningService

Service for downloading and consuming external data
Perl
1
star
80

ensembl-taxonomy

API for accessing NCBI taxonomy
Perl
1
star
81

ensembl-hive-htcondor

HTCondor Meadow for Ensembl Hive
Perl
1
star
82

ensembl-prodinf-djcore

Python
1
star
83

ensembl-prodinf-datachecks

JavaScript
1
star
84

ensembl-prodinf-tools

Python
1
star
85

ensembl-ontology-schema

Schema for the Ensembl ontology database
TSQL
1
star
86

ensembl-2020-static-assests

Static assets for new site
1
star
87

ensembl-git-test

Dummy repository to test git operations and scripts
1
star
88

ensembl-prodinf-legacy-core

Python
1
star
89

ensembl-dj-app

Django app template files
Python
1
star
90

fuse8

fuse8 for ensembl
C
1
star
91

gifts_rest

Python
1
star
92

ensembl-dj-project

Template to be reused when using django-admin startproject command
Python
1
star
93

thr

Second implementation of Trackhub Registry
Python
1
star
94

PerlModules

Perl
1
star
95

ensembl-genome-browser

Ensembl genome browser
JavaScript
1
star
96

ensembl-killlist

Perl
1
star
97

ensembl-prodinf-web

Web app for accessing Ensembl Production services
JavaScript
1
star
98

gene_finder

Jupyter Notebook
1
star
99

ensembl-external

*DEPRECATED* Code to load external data in the Ensembl website
Perl
1
star
100

ensembl-genes-nf

Ensembl Genebuild NextFlow pipelines
Nextflow
1
star