Bioinformatics
Showing 36 of 203 projects
A Ruby on Rails web application for querying and exploring drug-gene interaction data from The Genome Institute's database.
An open-source biomedical knowledge graph for drug discovery, precision medicine, and drug repurposing research.
A Python library for unsupervised learning of hidden semi-Markov models with explicit durations.
A GUI-based tool for training deep neural networks to segment biological images using corrective annotation.
A curated collection of resources for applying machine learning to biomedical and healthcare imaging applications.
A Python toolbox for analyzing smFISH microscopy images, including spot detection and cell segmentation.
An R package for image processing and analysis with a focus on microscopy and biological imaging.
A neural network model that integrates neighbor information from heterogeneous networks to discover new drug-target interactions.
An R package for 3D visualization and analysis of biological image data, especially single neuron tracings.
A large-scale foundation model pretrained on over 500,000 human bulk RNA-seq profiles for biomedical transcriptome analysis.
A PyTorch deep generative model for integrating and imputing single-cell multimodal data with missing modalities.
A machine learning approach for rapid, pathologist-level cell type annotation from spatial proteomics data like MIBI and CODEX.
Interactive visual pattern search and exploration tool for epigenomic data using unsupervised deep representation learning.
A multitask generative pre-trained language model for zero-shot cell type annotation, batch integration, and conditional cell generation in single-cell transcriptomics.
A curated list of academic papers, datasets, and metrics for 3D neurite segmentation in electron microscopy connectomics.
A lightweight image viewer for non-experts to interactively explore complex multiplexed tissue images.
A curated collection of software tools and databases for analyzing alternative splicing in genomics research.
A D3.js library for detecting peaks in noisy signals using continuous wavelet transform-based pattern matching.
Analyze your genetic data through natural language conversation with Claude, exploring health, ancestry, nutrition, and more from raw DNA files.
An interpretable multi-task deep neural network for single-cell multi-omics integration and cross-modal analysis.
An R package for processing and analyzing high-dimensional morphological profiling data from image-based cell biology.
An open-source pipeline for high-throughput, non-invasive extraction of phenotypic traits from plant images using deep learning.
A deep learning model that translates between single-cell multi-omic profiles, such as scATAC-seq and scRNA-seq, using a shared latent representation.
Pure Python library for reading NIS Elements ND2 microscopy images and metadata using the pims framework.
An OCaml library for building and executing typed, distributed scientific workflows with automatic dependency tracking.
Composable kernels for scikit-learn implemented in JAX, enabling faster kernel computations and automatic differentiation.
A Model Context Protocol server that provides AI assistants with structured scientific paper data including methods, results, and quality scores.
An MCP server that enables natural language conversation for analyzing spatial transcriptomics data through 60+ curated methods.
A machine learning pipeline that predicts 70 cell health phenotypes from Cell Painting image-based morphology profiles.
A Python library for integrating multiomic single-cell data using product-of-experts variational autoencoders.
A Python package for 3D single-cell shape analysis using geometric deep learning on point clouds and voxels.
An interactive image processing program for biologists written in Python.
A fast spatial deconvolution tool for transcriptomics data that scales to million-spot datasets while preserving rare cell type signals.
A modern Angular 20+ component library for Cytoscape.js graph visualization with dynamic forms and signal-based architecture.
A Quarto-powered blog for the Bioconductor community to share news, tutorials, and updates.
An R package for importing, analyzing, and visualizing single-particle tracking data from TrackMate XML outputs.
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