BluePyOpt

10x Genomics — commercial platform for single-cell and spatial genomics assays including Chromium single-cell RNA-seq (scRNA-seq), single-cell ATAC-seq, single-cell multiome (RNA+ATAC), Visium spatial

1 shared topic • 1 shared operation

chromVAR — R/Bioconductor package for determining variation in chromatin accessibility across sets of annotations or peaks. Designed for single-cell ATAC-seq (scATAC-seq) and sparse bulk ATAC-seq data

1 shared topic • 1 shared operation

ConsensusClusterPlus — R/Bioconductor package for determining cluster count and membership by stability evidence in unsupervised analysis, implementing the Monti et al. (2003) consensus clustering alg

1 shared topic • 1 shared operation

scater — Bioconductor single-cell RNA-seq QC and visualization toolkit built on SingleCellExperiment. Use when user needs per-cell QC metrics with addPerCellQCMetrics, adaptive MAD-based outlier detec

1 shared topic • 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

1 shared topic • 1 shared operation