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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

ZINB-WaVE (Zero-Inflated Negative Binomial Wave) for dimensionality reduction and normalization of single-cell RNA-seq data. Fits a zero-inflated negative binomial (ZINB) model to scRNA-seq count matr

1 shared topic • 3 shared operations

DRIMSeq is a Bioconductor R package for Differential Transcript Usage (DTU) analysis using a Dirichlet-multinomial distribution to model transcript-level count proportions. Tests whether relative tran

2 shared topics • 1 shared operation

WGCNA (Weighted Gene Co-expression Network Analysis) — R package for constructing weighted correlation networks from high-dimensional gene expression data. Identifies co-expression modules via hierarc

2 shared topics • 1 shared operation