35 Open source projects that are alternatives of or similar to ECLAIR

Code and Data to accompany "Dilated Convolutions for Modeling Long-Distance Genomic Dependencies", presented at the ICML 2017 Workshop on Computational Biology

screenlamp is a Python toolkit for hypothesis-driven virtual screening

The Biochemical Algorithms Library

Myokit: A simple interface to cardiac cellular electrophysiology

A standalone program that reads files created with the graphical network editor Escher and converts them to files in community standard formats.

An R Package for Geneset Enrichment Workflows

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.

A COBRApy extension for genome-scale models of metabolism and expression (ME-models)

Bioinformatics workflows developed for and used on the St. Jude Cloud project.

Towards fast and accurate SNP genotyping from whole genome sequencing data for bedside diagnostics.

Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling

Contact map analysis for biomolecules; based on MDTraj

📖 Generation and Applications of Knowledge Graphs in Systems and Networks Biology

Ultrafast sequence typing and gene detection from NGS raw reads

CPM implementation in pure JavaScript

A curated list of awesome computational cryo-EM methods.

Spatial alignment of single cell transcriptomic data.

A Curated List of Computational Biology Datasets Suitable for Machine Learning

Collection of scripts for bacterial genomics

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.

An integrated visual environment for metabolic modeling with common methods such as FBA, FVA and Elementary Flux Modes, and advanced features such as thermodynamic methods, extended Minimal Cut Sets, OptKnock, RobustKnock, OptCouple and more!

Syntax highlighting for computational biology

🧬 An R package for visualizing molecular data in 3D

The Microbiome Interpretable Temporal Rule Engine

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

A library to build and execute typed scientific workflows

Streamlining SLAM-seq analysis with ultra-high sensitivity

Fitness landscape exploration sandbox for biological sequence design.

A Go package for engineering organisms.

Clustering scRNAseq by genotypes

This is the main repository for the HackBio'2020 Virtual Internship Experience ❤️

Predicting protein structure through sequence modeling

pyQms, generalized, fast and accurate mass spectrometry data quantification

DeepChem 2017: Deep Learning & NLP for Computational Chemistry, Biology & Nano-materials

A prediction model for differential gene expression (DE) based on genome-wide regulatory interactions