Repository Index

Official repo for CellPLM: Pre-training of Cell Language Model Beyond Single Cells.

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

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

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

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 repository host gives no description.

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

The repository host gives no description.

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

The repository host gives no description.

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

PyTorch implementation of "TGSA: Protein-Protein Association-Based Twin Graph Neural Networks for Drug Response Prediction with Similarity Augmentation"

gateway for segmentation data to Rstats & visualization with ggplot2 - in development

• visualization
• fluorescence-data
• ggplot

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

Interpretable drug response prediction with graph neural networks over drugs, cell lines, and genes.