Repository Index

Native R and Python sample-deletion robustness for omics: candidate certificates, minimum deletion bounds, Bioconductor model refits and donor-level pseudobulk

• bioinformatics
• exact-optimization
• metabolomics
• paired-data

RNA-seq prediction with deep convolutional neural networks.

Bi-Directional Equivariant Long-Range DNA Sequence Modeling

Haplotype-aware CNV analysis from single-cell RNA-seq, ATAC-seq, and multiome

• cancer-genomics
• cnv-detection
• single-cell
• phylogeny

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

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

🏃 The go-to single-cell Foundation Model

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

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

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

Learning cell communication from spatial graphs of cells

• tensorflow
• gnn
• glm
• cvae

code to run sei and obtain sei and sequence class predictions

CASSIA: A Multi-Agent LLM-Based Single-Cell Cell Type Annotation Framework

• ai4science
• llm
• multiagent-systems
• prompt-engineering

Toolbox for the analysis of smFISH images.

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

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

The framework for quantification of neuronal anatomy

• neuroscience
• neuroanatomy-toolbox
• imagej
• imagej2

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

CancerFoundation: A single-cell RNA sequencing foundation model to decipher drug resistance in cancer

• cancer
• foundation-model
• single-cell

Data logistics system enabling real-time pathogen surveillance. Built for the Seattle Flu Study.

• postgres
• postgresql
• python
• infectious-disease

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

Analysis of cell migration in Igor Pro

• igor
• imagej
• cell-migration
• tracking

DeepAEG: A model for predicting cancer drug response based on data enhancement and edge-collaborative update strategies