425 Open source projects that are alternatives of or similar to biolink-api

phenol: Phenotype ontology library

CellO: Gene expression-based hierarchical cell type classification using the Cell Ontology

Feature extraction algorithm for genomic data

📊 Identify cell types and pathways affected by genetic risk loci.

Single Cell Analysis Pipelines

The Ensembl Compara Perl API and SQL schema

Internationalisation of the HPO content

📛 A Python package for using ontologies, terminologies, and biomedical nomenclatures

Streamlining SLAM-seq analysis with ultra-high sensitivity

Protwis is the backbone of the GPCRdb. The GPCRdb contains reference data, interactive visualisation and experiment design tools for G protein-coupled receptors (GPCRs).

A phenotype-based tool for variant prioritization in WES and WGS data

Computational Analysis of Novel Drug Opportunities

Classify sequencing reads using MinHash.

A simple command-line tool to download data from Joint Genome Institute databases

Implementation of Neural Distance Embeddings for Biological Sequences (NeuroSEED) in PyTorch (NeurIPS 2021)

Work in progress to design data models for UK Parliament

A curated list of phage related software and computational resources for phage scientists, bioinformaticians and enthusiasts.

information artifact ontology

Elastic, reproducible, and reusable genomic data science tools from R backed by cloud resources

A permissively licensed library designed to replace Illumina's Experiment Manager

NetworkX-based Python library for representing ontologies

This repository contains the dataset and the source code for the classification of food categories from meal images.

Natural language processing in examples and games

An R package for reproducible and automated ADMIXTOOLS analyses

Genomics using open source tools, running on GCP or AWS

The Common Core Ontology Repository holds the current released version of the Common Core Ontology suite.

Pathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform

Digital Cell Sorter (DCS): single cell RNA-seq analysis toolkit. Documentation:

Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads

Tibanna helps you run your genomic pipelines on Amazon cloud (AWS). It is used by the 4DN DCIC (4D Nucleome Data Coordination and Integration Center) to process data. Tibanna supports CWL/WDL (w/ docker), Snakemake (w/ conda) and custom Docker/shell command.

A faster lmm for GWAS. Supports GPU backend.

SIRIUS is a software for discovering a landscape of de-novo identification of metabolites using tandem mass spectrometry. This repository contains the code of the SIRIUS Software (GUI and CLI)

Learn interpretable computational phenotyping models from k-merized genomic data

A Kotlin DSL and library to create and plot RNA 2D structures

RO is an ontology of relations for use with biological ontologies

GRAph-based Finding of Individual Motif Occurrences

Gene fusion detection and visualization

Command line tool to run batch jobs concurrently with ETL framework on AWS or other cloud computing resources

A Python framework for integrating biological databases and structured data sources in Biological Expression Language (BEL)

dysgu-SV is a collection of tools for calling structural variants using short or long reads

Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline

Golang for Bioinformatics

R package for the recount2 project. Documentation website: http://leekgroup.github.io/recount/

The BridgeDb Library source code

Teaching material relevant to KGs

Improving genome bins through the combination of different binning programs

The knowledge of cloned rice genes lost in the information of rice functional genomics studies

GNparser normalises scientific names and extracts their semantic elements.

An NLP framework for clinical phenotyping. Docker | Python | Solr | OMOP. http://claritynlp.readthedocs.io/en/latest/

Open source Java library for computational proteomics

Tributech Catalog - Create and manage your DTDL models using our graphical interface and store them using our APIs.

A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment

📊 Codon usage tables in code-friendly format + Python bindings

Annotate DNA sequences for Gene Ontology terms

Automatic tagging and analysis of documents in an Apache Solr index for faceted search by RDF(S) Ontologies & SKOS thesauri

Structural variation caller using third generation sequencing

Haplotype VCF comparison tools

R mased batch sequence downloader, with primer development and in silico evaluation capabilities

Bioinformatics pipeline for SARS-CoV-2 sequencing at CZ Biohub

Simple pure Python SAM parser and objects for working with SAM records