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

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

An overview of algorithms for estimating pseudotime in single-cell RNA-seq data

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

🍺🔬 Bioinformatics formulae for the Homebrew package manager (macOS and Linux)

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.

Remote protein homology detection suite.

A faster lmm for GWAS. Supports GPU backend.

An ultrafast memory-efficient short read aligner

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)

Ultrafast de novo assembly for long noisy reads (though having no consensus step)

Learn interpretable computational phenotyping models from k-merized genomic data

🔬 BEDOPS: high-performance genomic feature operations

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

A community-maintained repository of cancer clinical knowledge bases and databases focused on cancer variants.

RO is an ontology of relations for use with biological ontologies

code for reading and processing Allen Institute for Brain Science data

GRAph-based Finding of Individual Motif Occurrences

A powerful open source data warehouse system

Gene fusion detection and visualization

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

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

The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.

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

GenomeTools genome analysis system.

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

Protein Graph Library

Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline

Python for Bioinformatics

Golang for Bioinformatics

Ten Quick Tips for Deep Learning in Biology

Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`

Genome assembly evaluation tool

The BridgeDb Library source code

Cuneiform distributed programming language

Teaching material relevant to KGs

Curated (meta)list of resources for Biology.

Improving genome bins through the combination of different binning programs

A repository for setting up a RNAseq workflow

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

Tools for working with genomic and high throughput sequencing data.

GNparser normalises scientific names and extracts their semantic elements.

Fast Reference-Guided Scaffolding of Genome Assembly Contigs. RagTag, the successor to RaGOO, is now available here: https://github.com/malonge/RagTag

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

Bioconductor cheat sheet

Open source Java library for computational proteomics

BioGrakn Knowledge Graph

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

MiXCR is a universal software for fast and accurate extraction of T- and B- cell receptor repertoires from any type of sequencing data. Free for academic use only.

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

Fast taxonomic classification of metagenomic sequencing reads using a protein reference database

Annotate DNA sequences for Gene Ontology terms

A curated list of bioinformatics bench-marking papers and resources.

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

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

Dash for Julia - A Julia interface to the Dash ecosystem for creating analytic web applications in Julia. No JavaScript required.

A curated list of Cheminformatics libraries and software.

Haplotype VCF comparison tools

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

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

Reproducible bioinformatics pipelines in python. Import any Unix tool/command in python.