10x Genomics

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

3 shared topics • 1 shared operation

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

SEACells — single-cell metacell identification using kernel archetypal analysis. Aggregates highly similar single cells into metacells that preserve transcriptional and epigenomic heterogeneity while

3 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

3 shared topics

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