398 Open source projects that are alternatives of or similar to React Cytoscapejs

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

Bayesian haplotype-based mutation calling

Cuneiform distributed programming language

BioGrakn Knowledge Graph

Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Salentin et al. (2015), https://www.doi.org/10.1093/nar/gkv315

Ten Quick Tips for Deep Learning in Biology

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

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

Fast multi-line FASTA/Q reader in several programming languages

A repository for setting up a RNAseq workflow

Bioconductor cheat sheet

Code examples of fast and simple k-mer counters for tutorial purposes

Python for Bioinformatics

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.

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

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

Genome assembly evaluation tool

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

code for reading and processing Allen Institute for Brain Science data

A comprehensive library for computational molecular biology

Curated (meta)list of resources for Biology.

GenomeTools genome analysis system.

ECG classification programs based on ML/DL methods

Tools for working with genomic and high throughput sequencing data.

The sources of the openSNP website

Single cell perturbation prediction

Deep learning infrastructure for bioinformatics

Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing

Python package for graph neural networks in chemistry and biology

Next generation sequencing reads de novo assembler.

Toolset for SV simulation, comparison and filtering

R package for analyzing single-cell RNA-seq data

Proof-of-concept seq-to-graph mapper and graph generator

Package for fetching metadata and downloading data from SRA/ENA/GEO

Reads simulator

parallel fastq-dump wrapper

RAxML Next Generation: faster, easier-to-use and more flexible

Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation

Rapid large-scale prokaryote pan genome analysis

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

A curated list of resources for learning bioinformatics.

MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. For documentation and downloading the program, please see the home page:

goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary

nim wrapper for htslib for parsing genomics data files

karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome

Simple simulation of single-cell RNA sequencing data

Annotated data.

fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"

Intuitive local web frontend for the BLAST bioinformatics tool

Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results

A genome browser that shows long reads and complex variants better

Syntax highlighting for computational biology

🔬 BEDOPS: high-performance genomic feature operations

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

A powerful open source data warehouse system

Protein Graph Library

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