Repository Index

Spatial Single Cell Analysis in Python

• single-cell-rna-seq
• single-cell-genomics
• spatial-transcriptomics
• spatial-analysis

Ankh: Optimized Protein Language Model

Open-source software for exploring and analyzing large, high-dimensional image-derived data.

• cellprofiler-analyst
• cellprofiler
• image-analysis
• machine-learning

TransformerCPI: Improving compound–protein interaction prediction by sequence-based deep learning with self-attention mechanism and label reversal experiments(BIOINFORMATICS 2020) https://doi.org/10.1093/bioinformatics/btaa524

• self-attention
• compound-protein-interaction
• transformercpi
• structure-free-virtual-sreening

Interpretable bilinear attention network with domain adaptation improves drug-target prediction.

Python package for image-based profiling

• cytominer
• microscopy
• morphological-profiling
• python

A tool for cell instance aware segmentation in densely packed 3D volumetric images

• segmentation
• deep-learning
• bioinformatics
• neural-network

Toolbox for the analysis of smFISH images.

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

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

Single-cell fluorescence microscopy data analysis

• microscopy
• fluorescence-microscopy-imaging

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

Official implementation of JAMIE, Joint variational Autoencoders for Multimodal Imputation and Embedding

• autoencoder
• imputation
• integration
• multimodal

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