Allen SDK

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

Use when working with Nebulosa, the R/Bioconductor package for recovering single-cell gene expression signals via kernel density estimation (KDE). Covers plot_density(), weighted KDE (WKDE), joint den

2 shared topics • 1 shared operation

openTSNE — modular Python library for t-distributed Stochastic Neighbor Embedding. Implements Barnes-Hut and FIt-SNE (interpolation-based) acceleration for scalable O(n log n) / near-linear t-SNE on l

2 shared topics • 1 shared operation

t-SNE (t-distributed Stochastic Neighbor Embedding) for nonlinear dimensionality reduction and visualization of high-dimensional data. Covers Barnes-Hut and exact modes, FIt-SNE/openTSNE interpolation

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