Repository Index

Deep probabilistic analysis of single-cell and spatial omics data

• scrna-seq
• variational-bayes
• variational-autoencoder
• cite-seq

The repository host gives no description.

• foundation-model
• gpt
• single-cell

Fast, sensitive and accurate integration of single-cell data with Harmony

• scrna-seq
• algorithm
• data-integration
• r

Spatial Single Cell Analysis in Python

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

R package for detecting doublets in single-cell RNA sequencing data

A tool for semi-automatic cell type classification

• python
• single-cell
• machine-learning
• scrna-seq

SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.

Graph-linked unified embedding for single-cell multi-omics data integration

• bioinformatics
• deep-learning
• single-cell
• single-cell-multiomics

Reference mapping for single-cell genomics

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

UCE is a zero-shot foundation model for single-cell gene expression data

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

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

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

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

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

A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.

Probabilistic cell segmentation for in situ spatial transcriptomics

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

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

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

🏃 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

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

Learning cell communication from spatial graphs of cells

• tensorflow
• gnn
• glm
• cvae

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

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