Repository Index

OCaml Bioinformatics Library

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

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

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

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

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 repository host gives no description.

MCP server for spatial transcriptomics analysis through natural language interfaces.

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

Deciphering cell-cell communication from spatially resolved transcriptomic data at single-cell resolution with subgraph-based attentional graph neural network

3D shape analysis using deep learning

• cancer-biology
• cell-biology
• deep-learning
• geometric-deep-learning

A versatile single-cell cross-modality translation method via dual-aligned variational autoencoders

Fast, deterministic cell-type deconvolution for million-bin spatial transcriptomics

• bioinformatics
• cell-type-deconvolution
• computational-biology
• deconvolution

A flexible Julia toolkit for high-dimensional cellular profiles

• julia
• morphological-analysis
• high-content-screening

scPair: Boosting single cell multimodal analysis by leveraging single cell atlases and implicit feature selection

XitoSBML - the spatial SBML plugin for ImageJ

• sbml
• systems-biology
• spatial-sbml-plugin
• imagej

Python library for statistical analysis of mRNA and protein distributions in fluorescent microscopy images