Repository Index

The repository host gives no description.

• foundation-model
• gpt
• single-cell

Segment Anything for Microscopy

• microscopy-images
• segment-anything
• segmentation
• cell-segmentation

Reference mapping for single-cell genomics

• single-cell
• deep-learning
• rna-seq-analysis
• data-integration

Pan-Cancer Integrative Histology-Genomic Analysis via Multimodal Deep Learning - Cancer Cell

• histology
• wsi-images
• pan-cancer-analysis
• genomics

This is the code for "Bitcoin Prediction" by Siraj Raval on Youtube

Usiigaci: stain-free cell tracking in phase contrast microscopy enabled by supervised machine learning

• tensorflow
• python3
• keras
• resnet-101

scPerturb: A resource and a python/R tool for single-cell perturbation data

• cite-seq
• database
• perturbation
• scatac-seq

Repository for Nicheformer: a foundation model for single-cell and spatial omics

🏃 The go-to single-cell Foundation Model

• batch-correction
• cell-biology
• celltype-annotation
• denoising

Code for "Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution", NeurIPS 2022.

• disentanglement
• drug-discovery
• genomics
• perturbation

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.

SplineDist: Automated Cell Segmentation with Spline Curves

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

Cell and line magic for PGF/TikZ-to-SVG rendering in Jupyter notebooks

• jupyter
• latex
• tikz
• tikz-figures

Jupyterlab extension to show notebook cell completion notifications

• jupyter
• jupyterlab
• browser-notifications
• jupyterlab-extension

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

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

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

Human Protein Atlas image classification competition

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