Bioinformatics
Showing 36 of 157 projects
A transformer-based model for predicting drug-target interactions using substructural pattern mining and augmented transformer encoders.
An R package to interact with NCBI's Entrez system, enabling programmatic search and retrieval of biological data.
Open-source software and data format standards for storing and manipulating biological light microscopy data.
A PyTorch-based segmentation toolbox for electron microscopy connectomics, enabling neural structure analysis in 3D volumes.
A computational pipeline that predicts drug-target interactions by learning low-dimensional vector representations from heterogeneous biological networks.
A Python package for easy molecular docking with a curated dataset and benchmark tasks for drug discovery.
An R package to programmatically retrieve chemical information from various web databases and APIs.
A Python API for downloading and processing neuroanatomical atlas data from multiple sources.
A Julia package providing core utilities for manipulating, comparing, and analyzing phylogenetic trees and networks.
A probabilistic cell segmentation method for spatial transcriptomics data from platforms like Xenium, CosMx, MERSCOPE, and Visium HD.
A Python library for blazing-fast, memory-efficient genomics data operations using DataFrames.
A resource and evaluation framework for benchmarking link prediction models on large-scale, heterogeneous biomedical knowledge graphs.
An R package for visualizing, adjusting, and comparing hierarchical clustering dendrograms.
A conversational AI framework for editing small molecules, peptides, and proteins using retrieval-augmented generation and domain feedback.
A deep learning model using transformer architecture to predict compound-protein interactions from molecular and protein sequences.
A deep bilinear attention network framework with adversarial domain adaptation for interpretable drug-target interaction prediction.
A large transformer foundation model for single-cell RNA sequencing data analysis, including gene network inference, denoising, and cell annotation.
A collection of reusable web components for visualizing biological data like protein sequences and features.
A Python package for processing and normalizing high-dimensional morphological feature data from high-throughput cell imaging experiments.
A curated collection of databases, software, and papers for computational biology research.
A Python library for interacting with QuPath, providing a pythonic interface to manage and analyze digital pathology projects.
A scikit-learn-compatible Python implementation of Multifactor Dimensionality Reduction (MDR) for feature construction.
A tool for cell instance aware segmentation in densely packed 3D volumetric images, originally developed for plant tissues.
A benchmark suite of protein sequence tasks to evaluate machine learning models for protein design.
A high-performance, user-friendly OCaml library for bioinformatics applications.
A knowledge-informed cross-species foundation model pre-trained on over 120 million human and mouse single-cell transcriptomes to decipher universal gene regulatory mechanisms.
A deep learning framework for predicting chromatin profiles and sequence regulatory activities from DNA sequences and variants.
A functional bioinformatics library for Scala providing strongly-typed DNA/RNA/protein sequences, transcription, translation, and alignment utilities.
Rust edit distance library accelerated with SIMD for fast Hamming, Levenshtein, and Damerau-Levenshtein calculations.
An open-source ImageJ plugin for automated processing, analysis, and visualization of single molecule localization microscopy (SMLM) data.
A suite of tools (wham and whamg) for sensitive and accurate structural variant detection and association testing from genomic sequencing data.
A performant JAX reimplementation of the UniRep model for generating protein sequence representations.
A curated list of resources for molecular docking, protein-protein docking, and related computational biology tasks.
A Python library for learning Bayesian network structure from observational and interventional data with support for missing values and parallel execution.
A pre-trained language model for single-cell RNA sequencing data that encodes cell-cell relations and accelerates inference for downstream tasks.
A Ruby on Rails web application for querying and exploring drug-gene interaction data from The Genome Institute's database.
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