Sqanti3

Cell Ranger — 10x Genomics official analysis pipeline for Chromium single-cell and spatial data. Performs FASTQ generation, alignment (STAR-based), barcode processing, UMI counting, V(D)J assembly, Fe

2 shared topics

cell2location — Bayesian spatial deconvolution mapping fine-grained cell types from scRNA-seq references onto spatial transcriptomics data. Estimates absolute cell type abundance per location via Pyro

2 shared topics

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

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

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