Seacells

Seurat — comprehensive R toolkit for single-cell genomics enabling QC, normalization (LogNormalize, SCTransform), feature selection, dimensionality reduction (PCA, UMAP, t-SNE), graph-based clustering

3 shared topics • 2 shared operations

Use when working with Conos (Clustering On Network Of Samples), the R package for joint analysis of multiple single-cell RNA-seq and spatial transcriptomics datasets. Covers building joint k-nearest-n

3 shared topics • 1 shared operation

scanpy-plots — visualization layer of the Scanpy single-cell RNA-seq analysis suite (scanpy.pl module). Generates UMAP, t-SNE, PCA embeddings, violin plots, dot plots, heatmaps, matrix plots, stacked

3 shared topics • 1 shared operation

scverse — the community-maintained Python ecosystem for single-cell and spatial omics analysis. Coordinates AnnData (universal data structure), scanpy (scRNA-seq QC/clustering/DE), squidpy (spatial tr

3 shared topics • 1 shared operation

STdeconvolve — reference-free cell-type deconvolution for spatial transcriptomics using Latent Dirichlet Allocation (LDA). Decomposes multi-cellular spatial pixels into cell-type proportions and trans

3 shared topics • 1 shared operation