Cellrank

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

2 shared topics • 2 shared operations

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 • 2 shared operations

IsoSeq — PacBio official full-length isoform sequencing pipeline for generating high-quality, full-length cDNA transcripts from PacBio SMRT/HiFi reads. Converts raw CCS reads through primer removal (l

2 shared topics • 1 shared operation

STARmap (Spatially-resolved Transcript Amplicon Readout mapping) — in situ spatial transcriptomics method that combines hydrogel-tissue chemistry with sequencing-by-hybridization (SEDAL) for multiplex

2 shared topics • 1 shared operation

stLearn — spatial transcriptomics analysis in Python integrating gene expression with tissue morphology. Provides SME (spatial morphological gene expression) normalization, spatial clustering, spatial

2 shared topics • 1 shared operation