SiT – spatial isoform transcriptomics
In situ capturing technologies add tissue context to gene expression data, with the potential of…
Browsing: Spatial Analysis
AllenDigger – spatial expression data visualization, spatial heterogeneity delineation, and single-cell registration based on the Allen Brain Atlas
Spatial transcriptomics can be used to capture cellular spatial organization and has facilitated new insights…
SRTsim – spatial pattern preserving simulations for spatially resolved transcriptomics
Spatially resolved transcriptomics (SRT)-specific computational methods are often developed, tested, validated, and evaluated in silico…
GraphST – spatially informed clustering, integration, and deconvolution of spatial transcriptomics
Spatial transcriptomics technologies generate gene expression profiles with spatial context, requiring spatially informed analysis tools…
Bulk2Space – de novo analysis of bulk RNA-seq data at spatially resolved single-cell resolution
Uncovering the tissue molecular architecture at single-cell resolution could help better understand organisms’ biological and…
STRIDE – a topic-model-based method to deconvolve spatial transcriptomics using scRNA-seq
The recent advances in spatial transcriptomics have brought unprecedented opportunities to understand the cellular heterogeneity…
Spacemake – processing and analysis of large-scale spatial transcriptomics data
Spatial sequencing methods increasingly gain popularity within RNA biology studies. State-of-the-art techniques quantify messenger RNA…
SPIRAL – Significant Process InfeRence ALgorithm for single cell RNA-sequencing and spatial transcriptomics
Gene expression data is complex and may hold information regarding multiple biological processes at once.…