A collection of tasks to probe the effectiveness of protein sequence representations in modeling aspects of protein design
- protein
- protein-sequences
- protein-design
- representation-learning
Repository Index
47,133 repositories indexed
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The repository host gives no description.
The repository host gives no description.
A tool for cell instance aware segmentation in densely packed 3D volumetric images
- segmentation
- deep-learning
- bioinformatics
- neural-network
GeneCompass
Learning cell communication from spatial graphs of cells
- tensorflow
- gnn
- glm
- cvae
code to run sei and obtain sei and sequence class predictions
Integrated pipeline for multiplexed image analysis
- multiplexed-imaging
- python
CASSIA: A Multi-Agent LLM-Based Single-Cell Cell Type Annotation Framework
- ai4science
- llm
- multiagent-systems
- prompt-engineering
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
TypeDB Bio: Biomedical Knowledge Graph
- bioinformatics
- knowledge-graph
- knowledge-base
- drug-discovery
BulkFormer: A large-scale foundation model for human bulk transcriptomes
NeoDTI: Neural integration of neighbor information from a heterogeneous network for discovering new drug-target interactions
- computational-biology
- bioinformatics
- graph-convolution
- deep-learning
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.
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
Run scripts, explore your genome, and get personalized explanations — all in natural dialogue.
- analysis
- claude
- claudecode
- dna
The repository host gives no description.
High-Dimensional Gene Expression and Morphology Profiles of Cells across 28,000 Genetic and Chemical Perturbations
Adaptive Graph Attention Auto-encoder for Spatial Domain Identification of Spatial Transcriptomics