Official repo for CellPLM: Pre-training of Cell Language Model Beyond Single Cells.
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PRnet is a flexible and scalable perturbation-conditioned generative model predicting transcriptional responses to unseen complex perturbations at bulk and single-cell levels.
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.
Repository for paper scMulan: a multitask generative pre-trained language model for single-cell analysis.
- foundation-models
- gpt
- single-cell
Adaptive Graph Attention Auto-encoder for Spatial Domain Identification of Spatial Transcriptomics
Deep learning model for single-cell inference of multi-omic profiles from a single input modality.
- single-cell
- scrna-seq
- scatac-seq
- deep-neural-networks
MCP server for spatial transcriptomics analysis through natural language interfaces.
- bioinformatics
- cell-communication
- deconvolution
- machine-learning
Multigrate: multiomic data integration for single-cell genomics
CancerFoundation: A single-cell RNA sequencing foundation model to decipher drug resistance in cancer
- cancer
- foundation-model
- single-cell
Deciphering cell-cell communication from spatially resolved transcriptomic data at single-cell resolution with subgraph-based attentional graph neural network
A versatile single-cell cross-modality translation method via dual-aligned variational autoencoders
Single-cell fluorescence microscopy data analysis
- microscopy
- fluorescence-microscopy-imaging
Fast, deterministic cell-type deconvolution for million-bin spatial transcriptomics
- bioinformatics
- cell-type-deconvolution
- computational-biology
- deconvolution
scPair: Boosting single cell multimodal analysis by leveraging single cell atlases and implicit feature selection