scater

Use when working with scCustomize — an R package providing enhanced, publication-quality visualization functions for single-cell RNA-seq data. Extends Seurat and ggplot2 with clustered dot plots, stac

2 shared topics • 2 shared operations

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

DecontX — R/Bioconductor method in the celda package for estimating and removing ambient RNA contamination from droplet-based single-cell RNA-seq data. Uses a Bayesian Dirichlet mixture model over cel

2 shared topics • 1 shared operation

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 • 1 shared operation

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 • 1 shared operation