R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics

High dimensional weighted gene co-expression network analysis

Haplotype-aware CNV analysis from single-cell RNA-seq, ATAC-seq, and multiome

A Toolbox for Spatial Transcriptomics Analysis

Associated code to the manuscript "Characterization of immune cell populations in the tumor microenvironment of colorectal cancer using high definition spatial profiling"

Code for the spatialLIBD R/Bioconductor package and shiny app

From geospatial to spatial -omics

characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular densities

Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).

Knowledge-graph-based cell-cell communication inference for spatially resolved transcriptomic data

Multiview Intercellular SpaTial modeling framework

Accurate and fast cell marker gene identification with COSG

Beyondcell is a computational methodology for identifying tumour cell subpopulations with distinct drug responses in single-cell RNA-seq and Spatial Transcriptomics data.

Profile purification of single-cell spatial transcriptomics data

R package for decontaminating the spot swapping effect and recovering true expression in spatial transcriptomics data

R-based Xenium Spatial Analysis Toolkit to assess gene expression gradients

Pipeline for SpatialTranscriptomics and 10X Visium data

Spatial Experiments raster - a rasterization preprocessing framework for scalable spatial omics data analysis

A pipeline for droplet-based single-cell RNA-seq and spot-based spatial transcriptomics data secondary analysis implemented in the drake Make-like pipeline toolkit for the R language.

Spatially-aware quality control for spatial transcriptomics