scvi-tools

SEACells — single-cell metacell identification using kernel archetypal analysis. Aggregates highly similar single cells into metacells that preserve transcriptional and epigenomic heterogeneity while

3 shared topics • 1 shared operation

scanpy-plots — visualization layer of the Scanpy single-cell RNA-seq analysis suite (scanpy.pl module). Generates UMAP, t-SNE, PCA embeddings, violin plots, dot plots, heatmaps, matrix plots, stacked

2 shared topics • 2 shared operations

liger (rliger) -- R package for integrative non-negative matrix factorization (iNMF) of single-cell multi-omic data. Integrates scRNA-seq, scATAC-seq, spatial transcriptomics, and methylation datasets

3 shared topics

scArches (Single-cell Architecture Surgery) — Python toolkit for reference-based single-cell data integration via transfer learning. Maps query datasets into pre-trained reference atlases using archit

2 shared topics • 1 shared operation

Seurat — comprehensive R toolkit for single-cell genomics enabling QC, normalization (LogNormalize, SCTransform), feature selection, dimensionality reduction (PCA, UMAP, t-SNE), graph-based clustering

2 shared topics • 1 shared operation