r3dmol🧬 An R package for visualizing molecular data in 3D
mitreThe Microbiome Interpretable Temporal Rule Engine
CellOCellO: Gene expression-based hierarchical cell type classification using the Cell Ontology
bistroA library to build and execute typed scientific workflows
slamdunkStreamlining SLAM-seq analysis with ultra-high sensitivity
FLEXSFitness landscape exploration sandbox for biological sequence design.
polyA Go package for engineering organisms.
pyqmspyQms, generalized, fast and accurate mass spectrometry data quantification
DeepChem-WorkshopDeepChem 2017: Deep Learning & NLP for Computational Chemistry, Biology & Nano-materials
DEcodeA prediction model for differential gene expression (DE) based on genome-wide regulatory interactions
ECLAIRRobust and scalable inference of cell lineages from gene expression data.
regulatory-predictionCode and Data to accompany "Dilated Convolutions for Modeling Long-Distance Genomic Dependencies", presented at the ICML 2017 Workshop on Computational Biology
screenlampscreenlamp is a Python toolkit for hypothesis-driven virtual screening
ballThe Biochemical Algorithms Library
myokitMyokit: A simple interface to cardiac cellular electrophysiology
EscherConverterA standalone program that reads files created with the graphical network editor Escher and converts them to files in community standard formats.
hypeRAn R Package for Geneset Enrichment Workflows
msk-STAPLESTAPLE (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.
cobrameA COBRApy extension for genome-scale models of metabolism and expression (ME-models)
workflowsBioinformatics workflows developed for and used on the St. Jude Cloud project.
vargenoTowards fast and accurate SNP genotyping from whole genome sequencing data for bedside diagnostics.
Clair3Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling
contact mapContact map analysis for biomolecules; based on MDTraj
doctoral-thesis📖 Generation and Applications of Knowledge Graphs in Systems and Networks Biology
STingUltrafast sequence typing and gene detection from NGS raw reads
artistooCPM implementation in pure JavaScript
TangramSpatial alignment of single cell transcriptomic data.
Jupyter DockJupyter Dock is a set of Jupyter Notebooks for performing molecular docking protocols interactively, as well as visualizing, converting file formats and analyzing the results.
CNApyAn 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!