Repository Index

OCaml Bioinformatics Library

Learning cell communication from spatial graphs of cells

• tensorflow
• gnn
• glm
• cvae

code to run sei and obtain sei and sequence class predictions

CASSIA: A Multi-Agent LLM-Based Single-Cell Cell Type Annotation Framework

• ai4science
• llm
• multiagent-systems
• prompt-engineering

Structural variant detection and association testing

Rails frontend to The Genome Institute's drug gene interaction database.

PRnet is a flexible and scalable perturbation-conditioned generative model predicting transcriptional responses to unseen complex perturbations at bulk and single-cell levels.

Toolbox for the analysis of smFISH images.

• pattern-classification
• rna-localization
• segmentation
• smfish

TypeDB Bio: Biomedical Knowledge Graph

• bioinformatics
• knowledge-graph
• knowledge-base
• drug-discovery

BulkFormer: A large-scale foundation model for human bulk transcriptomes

NeoDTI: Neural integration of neighbor information from a heterogeneous network for discovering new drug-target interactions

• computational-biology
• bioinformatics
• graph-convolution
• deep-learning

NeuroAnatomy Toolbox: An R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons.

• r
• neuroanatomy-toolbox
• cran
• neuron

PyTorch implementation of the MIDAS algorithm for single-cell multimodal data integration (Nature Biotechnology 2024).

• deep-generative-model
• deep-learning
• single-cell-data-integration
• single-cell-multiomics

Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.

Peax is a tool for interactive visual pattern search and exploration in epigenomic data based on unsupervised representation learning with autoencoders

• epigenomics
• pattern-search
• data-visualization
• interactive-machine-learning

Machine learning for Analysis of Proteomics in Spatial biology - Nature Communications

• cell-annotation
• multiplexed-imaging
• mpif

Repository for paper scMulan: a multitask generative pre-trained language model for single-cell analysis.

• foundation-models
• gpt
• single-cell

The framework for quantification of neuronal anatomy

• neuroscience
• neuroanatomy-toolbox
• imagej
• imagej2

Run scripts, explore your genome, and get personalized explanations — all in natural dialogue.

• analysis
• claude
• claudecode
• dna

High-Dimensional Gene Expression and Morphology Profiles of Cells across 28,000 Genetic and Chemical Perturbations

Tool for precise, interactive, fast and scalable FISH spot detection

Adaptive Graph Attention Auto-encoder for Spatial Domain Identification of Spatial Transcriptomics

The repository host gives no description.

MCP server for spatial transcriptomics analysis through natural language interfaces.

• bioinformatics
• cell-communication
• deconvolution
• machine-learning