dittoSeq

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

2 shared topics • 1 shared operation

CellChat — R package for inference, analysis, and visualization of cell-cell communication networks from single-cell RNA-seq data. Uses a curated ligand-receptor database (CellChatDB) to quantify sign

2 shared topics • 1 shared operation

Cumulus — cloud-based framework for large-scale single-cell and single-nucleus RNA-seq analysis on Terra/Google Cloud. Provides WDL workflows for demultiplexing (demuxEM, souporcell, demuxlet), count

2 shared topics • 1 shared operation

DoRothEA — Discriminant Regulon Expression Analysis R/Bioconductor package for transcription factor (TF) activity inference from gene expression data. Provides curated TF regulons (confidence levels A

2 shared topics • 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

2 shared topics • 1 shared operation