Cumulus

Use when working with batchelor — the Bioconductor R package for batch correction of single-cell RNA-seq data. Removes batch effects using mutual nearest neighbours (fastMNN, mnnCorrect), linear resca

2 shared topics • 2 shared operations

Pegasus — scalable single-cell RNA-seq analysis toolkit for millions of cells. Command-line tool and Python package for preprocessing, batch correction, clustering, differential expression, visualizat

2 shared topics • 2 shared operations

scDblFinder — Bioconductor R package for detecting doublets in single-cell RNA-seq data using simulation-based classification with gradient boosting. Identifies neotypic and heterotypic doublets in dr

2 shared topics • 2 shared operations

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