LIANA

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

2 shared topics • 2 shared operations

NicheNet — R-based computational framework for studying intercellular communication from single-cell transcriptomics. Predicts which ligands expressed by sender cell types regulate target gene express

2 shared topics • 2 shared operations

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

2 shared topics • 2 shared operations

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

STARmap (Spatially-resolved Transcript Amplicon Readout mapping) — in situ spatial transcriptomics method that combines hydrogel-tissue chemistry with sequencing-by-hybridization (SEDAL) for multiplex

2 shared topics • 1 shared operation