121 Open Source Computational Biology Software Projects
Free and open source computational biology code projects including engines, APIs, generators, and tools.
Opensim Core 494 ⭐
SimTK OpenSim C++ libraries and command-line applications, and Java/Python wrapping.
Open Computational Neuroscience Resources 301 ⭐
A publicly-editable collection of open computational neuroscience resources
Awesome Computational Neuroscience 355 ⭐
A list of schools and researchers in computational neuroscience
Clairvoyante 159 ⭐
Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing
Sorgerlab Indra 126 ⭐
INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.
Clair 88 ⭐
Clair: Exploring the limit of using deep neural network on pileup data for germline variant calling
Neodti 56 ⭐
NeoDTI: Neural integration of neighbor information from a heterogeneous network for discovering new drug-target interactions
Compbiodatasetsformachinelearning 63 ⭐
A Curated List of Computational Biology Datasets Suitable for Machine Learning
Skyhawk 32 ⭐
An Artificial Neural Network-based discriminator for validating clinically significant genomic variants
Montilab Pipeliner 36 ⭐
A flexible Nextflow-based framework for the definition of sequencing data processing pipelines
Forester 28 ⭐
forester is a collection of open source libraries of Java and Ruby software for phylogenomics and evolutionary biology research
Regulatory Prediction 25 ⭐
Code and Data to accompany "Dilated Convolutions for Modeling Long-Distance Genomic Dependencies", presented at the ICML 2017 Workshop on Computational Biology
Dieterich Lab Dcc 30 ⭐
DCC uses output from the STAR read mapper to systematically detect back-splice junctions in next-generation sequencing data. DCC applies a series of filters and integrates data across replicate sets to arrive at a precise list of circRNA candidates.
Soap3 Dp 25 ⭐
To tackle the exponentially increasing throughput of Next-Generation Sequencing (NGS), most of the existing short-read aligners can be configured to favor speed in trade of accuracy and sensitivity. SOAP3-dp, through leveraging the computational power of both CPU and GPU with optimized algorithms, delivers high speed and sensitivity simultaneously.
Ibrahimtanyalcin Lexicon 28 ⭐
Data visualization library for creating interactive graphs and dashboards for bioinformatics etc.
Soapdenovo Trans 25 ⭐
SOAPdenovo-Trans, a de novo transcriptome assembler designed specifically for RNA-Seq. We evaluated its performance on transcriptome datasets from rice and mouse.
Deepchem Workshop 22 ⭐
DeepChem 2017: Deep Learning & NLP for Computational Chemistry, Biology & Nano-materials
Doctoral Thesis 24 ⭐
📖 Generation and Applications of Knowledge Graphs in Systems and Networks Biology
Bohdan Khomtchouk Microscope 20 ⭐
ChIP-seq/RNA-seq analysis software suite for gene expression heatmaps
Pterasoftware 70 ⭐
Ptera Software is a fast, easy-to-use, and open-source software package for analyzing flapping-wing flight.
Team Rosalind Project 22 ⭐
This is the main repository for the HackBio'2020 Virtual Internship Experience ❤️
Aptasuite 20 ⭐
A full-featured bioinformatics software collection for the comprehensive analysis of aptamers in HT-SELEX experiments.
Vargeno 17 ⭐
Towards fast and accurate SNP genotyping from whole genome sequencing data for bedside diagnostics.
Iodata 69 ⭐
Python library for reading, writing, and converting computational chemistry file formats and generating input files.
Phylotoast 12 ⭐
Tools for phylogenetic data analysis including visualization and cluster-computing support.
Escherconverter 13 ⭐
A standalone program that reads files created with the graphical network editor Escher and converts them to files in community standard formats.
Review 16 ⭐
:earth_americas: Review materials for bioinformatics, computational biology, and science in general
Coursera Computational Neuroscience 38 ⭐
Coursera Computational-NeuroScience course of the University of Washington
Causalpath 20 ⭐
A project for exploring differentially active signaling paths related to proteomics datasets
Deweylab Cello 34 ⭐
CellO: Gene expression-based hierarchical cell type classification using the Cell Ontology
Jupyter_dock 116 ⭐
Jupyter Dock is a set of Jupyter Notebooks for performing molecular docking protocols interactively, as well as visualizing, converting file formats and analyzing the results.
Metagem 67 ⭐
:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
Clair3 76 ⭐
Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling
Msk Staple 34 ⭐
STAPLE (Shared Tools for Automatic Personalised Lower Extremity modelling) consists of a collection of methods for generating skeletal models from three-dimensional bone geometries, usually segmented from medical images. The methods are currently being expanded to create complete musculoskeletal models.