Bioconductor Packages

Spatial transcriptomic clustering

Identify Batch-Biased Spatially Variable Genes

Swiss-army toolkit for selecting niche fronts and invasive margins in spatial transcriptomics data

Infer Ligand-Receptor Interactions from bulk expression (transcriptomics/proteomics) data, or spatial transcriptomics

Spatially Informed Cell Type Deconvolution for Spatial Transcriptomics

Identification of cell-type-specific spatially variable genes accounting for excess zeros

This package provides methods for analysing spatial transcriptomics data and for discovering gene clusters

DESpace: a framework to discover spatially variable genes and differential spatial patterns across conditions

DenoIST: Denoising Image-based Spatial Transcriptomics data

A Correlation Based Multiview Self Organizing Maps Clustering For IMC Datasets

NanoString GeoMx Tools

HiCPotts: Hierarchical Modeling to Identify and Correct Genomic Biases in Hi-C

Hierarchical Inference of Spatial Positions from Hi-C Data

Plotting functionality for Histopathology pipeline datasets

Interface to 'HuBMAP'

Prioritising a molecule-level storage of Spatial Transcriptomics Data

OSTA book data

Rank-based reference mapping for fast and robust cell type annotation in spatial and single-cell transcriptomics

Investigating regions of interest and performing regional cell type-specific analysis with spatial transcriptomics data

Rasterization Preprocessing Framework for Scalable Spatial Omics Data Analysis

Spatial Image Analysis of Tissues

`SPOTlight`: Spatial Transcriptomics Deconvolution

Predicting cell states and their variability in single-cell or spatial omics data

Spatial Neighborhood Modeling and Differential Expression Analysis for Transcriptomics

Spatially-aware normalisation for spatial transcriptomics data

Spatial Interaction Markers

SpaceTrooper performs Quality Control analysis of Image-Based spatial

Identification and Classification of Spatial Artifacts in Visium and Visium HD Data

Deconvolution of mixed cells from spatial and/or bulk gene expression data

S4 Class for Spatially Resolved -omics Data

Read in Xenium, CosMx, MERSCOPE or STARmapPLUS data as SpatialExperiment object

Integrating SpatialExperiment with Simple Features in sf

Spatial Overlay for Omic Data from Nanostring GeoMx Data

SpotClean adjusts for spot swapping in spatial transcriptomics data

Spatially-aware quality control for spatial transcriptomics

A package to identify changes in cell state relative to spatial associations

Import Visium data from the 10X Space Ranger pipeline

From geospatial to spatial omics

Import and represent Xenium data from the 10X Xenium Analyzer

Language agnostic on disk serialization of SpatialFeatureExperiment

A Hidden Markov Model Approach for Identifying Differentially Methylated Sites and Regions for Beta-Valued DNA Methylation Data

ClustSIGNAL: a spatial clustering method

Identify Spatial Homogeneous Regions with concordex

An interactive multi-channel image viewer for R

Unified multi-dimensional visualizations with Gestalt principles

Visualizing Single Cell and Spatial Transcriptomics

Visualization functions for spatial transcriptomics data

Spatial cellular neighbourhood scanning in R

Methods for imaging mass cytometry data analysis

Finding spatially relevant marker genes in image based spatial transcriptomics data