ensembl

There are 3 repositories under ensembl topic.

gget
pachterlab / gget
🧬 gget enables efficient querying of genomic reference databases
alphafold alphafold2 archs4 blast databases enrichment-analysis enrichr ensembl gget ncbi reference uniprot
Language:Python 949
genomepy
vanheeringen-lab / genomepy
genes and genomes at your fingertips
bioconda ensembl genome ncbi python ucsc
Language:Python 382
pyGeno
tariqdaouda / pyGeno
Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
bed bioinformatics biology cancer cancer-genomes cancer-genomics csv-parser ensembl genome genome-annotation genome-browser genome-sequencing genomes genomics gtf medical medicine proteomics snps vcf
Language:Python 311
Ensembl / ensembl-hive
EnsEMBL Hive - a system for creating and running pipelines on a distributed compute resource
ensembl workflow-management-system perl python mysql sqlite postgresql high-performance-computing pipeline ehive docker slurm
Language:Perl 52
Ensembl / ensembl-compara
The Ensembl Compara Perl API and SQL schema
ensembl perl api comparative-genomics mysql database bioinformatics
Language:Perl 51
ding-lab / hotspot3d
3D hotspot mutation proximity analysis tool
mutations perl 3d-proximity proximity-search clustering protein-structure hotspot analysis cancer genomic disease drug ensembl uniprot blat hgnc pymol drugport drugbank
Language:Perl 46
biomaRt
grimbough / biomaRt
R package providing query functionality to BioMart instances like Ensembl
bioconductor biomart ensembl r
Language:R 36
jorainer / ensembldb
This is the ensembldb development repository.
bioconductor bioconductor-packages ensembl annotation
Language:R 33
noamteyssier / ggetrs
Efficient querying of biological databases
bioinformatics command-line-tool enrichr ensembl rust uniprot
Language:Rust 28
gawbul / pyEnsemblRest
A client for the Ensembl REST API written in the Python programming language
python bioinformatics ensembl ensembl-genomes ensembl-rest rest-client rest
Language:Python 26
Ensembl / treebest
TreeBeST: Tree Building guided by Species Tree (Ensembl Compara modifications)
phylogeny maximum-likelihood neighbor-joining reconciliation ensembl gene-trees species-trees
Language:C 21
robinvanderlee / positive-selection
Scripts and procedures for detecting positively selected genes and codons in primates
bioinformatics bioinformatics-pipeline bioinformatics-scripts bioinformatics-analysis computational-biology evolution comparative-genomics positive-selection primates genetics sequence-alignment genomics genomes genome-analysis codeml immunity ensembl
Language:Perl 19
related-sciences / ensembl-genes
Extract the Ensembl genes catalog to simple tables
bioinformatics ensembl genes human mouse rat sql
Language:Python 17
pwilmart / fasta_utilities
Utilities for downloading and managing protein FASTA files.
ensembl fasta ncbi protein-databases python3 uniprot
Language:Python 13
bigbio / py-pgatk
Python tools for proteogenomics analysis toolkit
python proteogenomics ensembl proteomics mass-spectrometry vcf proteogenomics-analysis-toolkit
Language:Python 10
Ensembl / ensembl-git-tools
A collection of tools which Ensembl uses to work with Git
ensembl git
Language:Perl 9
worst-genbank-ever
TimothyStiles / worst-genbank-ever
The most awful genbank file you'll ever need to parse.
genbank genbank-files ensembl ddbj
9
stevekm / reference-annotations
Makefile for reference annotations for genes & genomic regions
annotations bioinformatics ensembl gencode genome genomic-regions human makefile reference-annotation reference-data
Language:Makefile 8
Ensembl / trackhub-registry
Specifications and implementation of the TrackHub registry
registry perl genome-browser ensembl trackhubs catalyst elasticsearch ucsc das
Language:Perl 7
Ad115 / ICGC-data-parser
To automate data collection from ICGC database.
icgc perl ensembl
Language:Jupyter Notebook 6
danilotat / UTR_add_extend_GTF
Provided tool will add explicit 3'UTR and extends it into a valid Ensembl GTF file. It's useful for 3'RNAseq when 3' coordinates might not be as good as you expect.
bioinformatics rna-seq 3-rna-seq differential-expression gtf ensembl
Language:Python 5
bridgedb / create-bridgedb-genedb
Example of script to query BioMart, parse and create a BridgeDb database
ensembl gene identifier-mapping
Language:Java 4
patterninstitute / ensemblr
R client to the Ensembl REST API
ensembl ensembl-rest
Language:R 4
rohitxsh / ensembl_lakehouse_ui
Ensembl's data lakehouse frontend | GSoC '22
ensembl genome google-summer-of-code gsoc gsoc-2022 react reactjs material-ui tailwindcss
Language:TypeScript 4
antonkulaga / genotations
A small library to work with ensembl and other annotations in python
annotations bioinformatics ensembl genes genomics gtf polars transcriptomics
Language:Python 3
Ensembl / ensembl-hive-pbspro
'PBS Pro' implementation of Ensembl Hive Meadow interface
ehive pbspro pbs-pro pbs perl docker ensembl
Language:Perl 3
ainefairbrother / ensemblQueryR
Package allowing easy integration of Ensembl querying with your R workflow
ensembl ld r api-rest bioinformatics
Language:R 2
bigbio / pgdb
ProteomeGenomics Database Creation - Nextflow Pipeline
proteogenomics nf-core nextflow mass-spectrometry proteomics ensembl cosmic
Language:Nextflow 2
chanakaDe / ensembl-public-rest
Public REST API (Endpoint for testing purposes) for Ensembl Gene Autocompetion Table
python flask flask-restful sqlalchemy genes rest-api ensembl
Language:Python 2
chanakaDe / ensembl-ui
This application is created to query track infomation using provided data sources. (Ensembl Elastic-Search data source). Users can query throgh this application using provided parameters.
angularjs heroku gulp jquery ensembl bootstrap
Language:JavaScript 2
eggzilla / BiobaseHTTPTools
Tools for querying bioinformatics web resources
bioinformatics ncbi ensembl
Language:Haskell 2
mateuspatricio / ensembl-retreat-2018
Some files used by the "MPI/multi-threaded software in eHive/LSF" session during the Ensembl retreat 2018
cpp ehive ensembl mpi
Language:Perl 2
nthomasCUBE / Gexplora
Gexplora - user-interface to analyse genomic elements along chromosomes
numpy chromosomes heatmap python tkinter stringdb oma ensembl linechart cis-element gtf annotation
Language:Python 2
rohitxsh / ensembl_lakehouse
Ensembl's data lakehouse backend | GSoC '22
ensembl gsoc-2022 aws boto3 celery genome google-summer-of-code gsoc pandas python python3 fastapi
Language:Python 2
rohitxsh / sql2parquet_py
Python script to migrate genomic data from MySQL DB to parquet files (with added support to upload output files to AWS S3) | GSoC '22
gsoc-2022 ensembl aws boto3 genome pandas parquet python python3 google-summer-of-code gsoc
Language:Python 2
vizport / vizgvar-v1
Explore protein variation data from the Ensembl API in a simple, yet very effective and easy to use way.
bioinformatics d3js ensembl
Language:JavaScript 2

ensembl

pachterlab / gget

vanheeringen-lab / genomepy

tariqdaouda / pyGeno

Ensembl / ensembl-hive

Ensembl / ensembl-compara

ding-lab / hotspot3d

grimbough / biomaRt

jorainer / ensembldb

noamteyssier / ggetrs

gawbul / pyEnsemblRest

Ensembl / treebest

robinvanderlee / positive-selection

related-sciences / ensembl-genes

pwilmart / fasta_utilities

bigbio / py-pgatk

Ensembl / ensembl-git-tools

TimothyStiles / worst-genbank-ever

stevekm / reference-annotations

Ensembl / trackhub-registry

Ad115 / ICGC-data-parser

danilotat / UTR_add_extend_GTF

bridgedb / create-bridgedb-genedb

patterninstitute / ensemblr

rohitxsh / ensembl_lakehouse_ui

antonkulaga / genotations

Ensembl / ensembl-hive-pbspro

ainefairbrother / ensemblQueryR

bigbio / pgdb

chanakaDe / ensembl-public-rest

chanakaDe / ensembl-ui

eggzilla / BiobaseHTTPTools

mateuspatricio / ensembl-retreat-2018

nthomasCUBE / Gexplora

rohitxsh / ensembl_lakehouse

rohitxsh / sql2parquet_py

vizport / vizgvar-v1