369 Open source projects that are alternatives of or similar to Ontologies

Scalable genomic data analysis.

Compressor for genomic files (FASTQ, SAM/BAM, VCF, FASTA, GVF, 23andMe...), up to 5x better than gzip and faster too

A Java API for high-throughput sequencing data (HTS) formats.

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs

Feature Annotation Location Description Ontology

A collection of scripts and notes related to genomics and bioinformatics

find large indels (in the blind spot between GATK/freebayes and SV callers)

A DNA Sequence Alignment/Map (SAM) library for Clojure

Frequently used commands in bioinformatics

Efficient variant-call data storage and retrieval library using the TileDB storage library.

annotate a VCF with other VCFs/BEDs/tabixed files

simple viewer for variant call format using htslib

Haplotype VCF comparison tools

cython + htslib == fast VCF and BCF processing

Bayesian genotyper for structural variants

Spark VCF data source implementation for Dataframes

An ontology of cell types

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

Version 2.1.0 released

Cyber-investigation Analysis Standard Expression (CASE) Ontology

An interactive web portal for exploring immuno-oncology data

Provide R access to the NCI Genomic Data Commons portal.

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch

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

(WIP) best-practices workflow for rare disease

Global Insurance Ontology

Data Wrangling and Processing for Genomics

Method to optimally select samples for validation and resequencing

Ontology Enhancement Proposal

Assembling the cause of phenotypes and genotypes from NGS data

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

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.

PERF is an Exhaustive Repeat Finder

Genotyping of segregating mobile elements insertions

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

Compute N50/NG50 and auN/auNG

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

An open-access bioinformatics text

Toolkit for preparing genomes for submission to NCBI

A package for designing compact and comprehensive capture probe sets.

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

A faster lmm for GWAS. Supports GPU backend.

Introduction to Cloud Computing for Genomics

netSmooth: A Network smoothing based method for Single Cell RNA-seq imputation

Python API for comprehensive GWAS analysis using GEMMA

Data transformation framework for LinkML data models

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

My collection of light bioinformatics analysis pipelines for specific tasks

Complex structural variant detection from WGS data

Chanjo provides a better way to analyze coverage data in clinical sequencing.

A modular annotation tool for genomic variants

Genetic Map Comparison

The Go Language Implementation of Ontology Actor Model

Environmental DNA metabarcoding taxonomic identification

pythonic wrapper for htslib

SaffronTree: Reference free rapid phylogenetic tree construction from raw read data

InterARTIC - An interactive local web application for viral whole genome sequencing utilising the artic network pipelines..

Fast alignment and preprocessing of chromatin profiles

Annotation of VCF variants with functional impact and from databases (executable+library)