SingleR

Azimuth — reference-based automated cell type annotation for single-cell RNA-seq. Maps a query Seurat object or h5ad dataset onto a curated reference atlas (PBMC, lung, kidney, cortex, heart, bone mar

2 shared topics • 1 shared operation

celltypist — automated cell type annotation for single-cell RNA-seq data using pre-trained logistic regression models from a curated model zoo. Use for: cell type classification, immune cell annotatio

2 shared topics • 1 shared operation

WARP (WDL Analysis Research Pipelines) — Broad Institute's cloud-optimized collection of genomics pipelines written in WDL (Workflow Description Language). Covers whole-genome sequencing (WGS), whole-

2 shared topics • 1 shared operation

scJoint integrates atlas-scale single-cell RNA-seq and scATAC-seq data using transfer learning. Transfers cell type labels from annotated RNA datasets to unannotated ATAC datasets via joint neural net

2 shared topics • 1 shared operation

UCE (Universal Cell Embeddings) — species-agnostic cell embedding model from Stanford SNAP Lab that uses protein language models (ESM-2) to create universal cell representations without species-specif

2 shared topics • 1 shared operation