Scanpy

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

Giotto Suite — R toolkit for spatial multi-omics analysis at all scales and resolutions. Processes data from Visium, MERFISH, Xenium, CosMx, Slide-seq, CODEX, Stereo-seq, and other spatial technologie

1 shared topic • 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

1 shared topic • 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

1 shared topic • 2 shared operations

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

1 shared topic • 2 shared operations