Ensembl/VEP_plugins

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Created about 13 years ago
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Ensembl/VEP_plugins

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Plugins for the Ensembl Variant Effect Predictor (VEP)

Ensembl Variant Effect Predictor - Plugins

This repository holds plugins which are developed to extend the functionality of the Ensembl Variant Effect Predictor (VEP). See here for the core VEP code.

Usage

Please refer to the documentation in each file for details of what each plugin does and how to run it. At minimum, you will need to put the module in your ~/.vep/Plugins directory (or elsewhere on your $PERL5LIB) and then run the VEP with the argument --plugin .

Documentation

VEP documentation has general information on installing and running VEP.
VEP plugin documentation details how plugins are developed and used.

Contact Us

Please create a separate issue for each query.

Comments or questions can also be sent to the Ensembl Helpdesk at:

https://www.ensembl.org/Help/Contact.

ensembl-vep

The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants

WiggleTools

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

ensembl-rest

Language agnostic RESTful data access to Ensembl data over HTTP

ensembl

The Ensembl Core Perl API and SQL schema

ensembl-pipeline

*DEPRECATED* Job management for the Ensembl Genebuild pipeline

ensembl-hive

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

ensembl-compara

The Ensembl Compara Perl API and SQL schema

postgap

Linking GWAS studies to genes through cis-regulatory datasets

Jupyter Notebook

plant-scripts

Scripting analyses of genomes in Ensembl Plants

ensembl-tools

ensembl-variation

The Ensembl Variation Perl API and SQL schema

Bio-DB-HTS

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

ensembl-webcode

The code to run an Ensembl website

ensembl-funcgen

Ensembl Funcgen Perl API and SQL schema

ensembl-analysis

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

ensembl-client

Ensembl beta client

ensj-healthcheck

Ensembl's Automated QC Framework

ensembl-production

Ensembl Production code

ensembl-anno

ensembl-git-tools

A collection of tools which Ensembl uses to work with Git

public-plugins

Plugins for an Ensembl website

ensembl-io

File parsing and writing code for Ensembl

ensembl-genomio

Pipelines to turn basic genomic data into Ensembl cores and back

treefam_tools

This folder contains scripts to access/use the TreeFam database

XML-To-Blockly

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

homebrew-ensembl

Core formula for Ensembl

trackhub-registry

Specifications and implementation of the TrackHub registry

plant_tools

Tools and documentation for Plants

EpiRR

A registry of epigenomics reference data sets

ols-client

ensembl-xs

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

ensembl-test

Test libraries and harnesses used for running the Ensembl test suite

ensembl-datacheck

Code for checking Ensembl databases during release production

ensembl-database-loader

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

rest-api-jupyter-course

Python and R notebooks to be used by Jupyter

Jupyter Notebook

ensembl-metadata

API for storing and querying metadata from Ensembl and EnsemblGenomes

guiHive

Graphical interface for the eHive workflow manager

ensembl-py

Python Ensembl code source repository

ensembl-web-docker

ensembl-web docker

tark

homebrew-external

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

ensembl-genes

Python Ensembl Gene Annotation code source repository

ensc-core

C API for the Ensembl Database

GIFTS

ensembl-biomart

Code to build the ensembl and ensembl genomes marts

ensembl-rest-deploy

Tools for automatic server deployment

homebrew-cask

Meta formulas for homebrew/linuxbrew

ensembl-doc

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

ensembl-utils

Ensembl python utils

ensembl-presentation

Presentations used in Ensembl workshops

gene_symbol_transformer

Transformer model for gene symbol assignment of protein coding sequences

ensembl-otter

ensembl-hive-pbspro

'PBS Pro' implementation of Ensembl Hive Meadow interface

ensembl-annotation

The Ensembl gene annotation pipeline (a work in progress)

homebrew-moonshine

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

ensembl-production-services

Ensembl production service portal

gsoc-dl-protein-coding-genes

ensembl-2020-server

Ensembl 2020 server backend

Bio-DB-Big

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

ensembl-metadata-registry

REST API for ensembl-metadata

repeat_nf

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

ensembl-datacheck-py

ensembl-glossary

ensembl-hdf5

Wrapper for the storage of large numerical arrays

cwl-udocker-tests

A repository for testing udocker, cwl and toil

ensembl-2020-genome-search

Genome search backend microservice for ensembl 2020

homebrew-icc

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

gene_pcp

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

cpanfiles

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

python-requirements

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

gti-genesearch

Query manager and REST interface to Advanced Search

webvm

ensembl-thoas

Son of Ariadne, a GraphQL server and supporting software

pantherScore

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

treefam-webcode

Web-code for the TreeFam website

ensembl-production-metazoa

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

Finemap

VersioningService

Service for downloading and consuming external data

ensembl-taxonomy

API for accessing NCBI taxonomy

ensembl-hive-htcondor

HTCondor Meadow for Ensembl Hive

ensembl-prodinf-djcore

ensembl-prodinf-datachecks

ensembl-prodinf-tools

ensembl-ontology-schema

Schema for the Ensembl ontology database

ensembl-2020-static-assests

Static assets for new site

ensembl-git-test

Dummy repository to test git operations and scripts

ensembl-prodinf-legacy-core

ensembl-dj-app

Django app template files

fuse8

fuse8 for ensembl

gifts_rest

ensembl-dj-project

Template to be reused when using django-admin startproject command

thr

Second implementation of Trackhub Registry

PerlModules

ensembl-genome-browser

Ensembl genome browser

ensembl-killlist

ensembl-prodinf-web

Web app for accessing Ensembl Production services

gene_finder

Jupyter Notebook

ensembl-external

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

ensembl-genes-nf

Ensembl Genebuild NextFlow pipelines

seqtools