awesome-spatial-omics

This wants to be a community maintained repository for collecting single-cell spatial omics resources to stay updated with this fast-growing field.

Any contribution is really appreciated.

At the moment we distinguish these main sections:

• Spatial Omics Technologies
  • Spatial Transcriptomics
  • Spatial Multi Modal
  • Others (if any)
• Spatial Omics Methods & Tools
  • Spatial Transcriptomics Methods & Tools
  • Spatial Multi Modal Methods & Tools
  • Others (if any)

This repo is inspired to the Mike Love's Awesome Multi Omics and the Sean Davis' Awesome Single Cell ones.

Spatial Omics Technologies

This section is referred to all the technologies that can be collected regarding the spatial omics field, each of this subsections could collect two main families of this technologies, spot-based and molecular-based.

Spatial Transcriptomics

Spot-Based
2016	10x Visium	Allows the detection of transcripts at spatial spot level	Ståhl et al.
2019	HDST	High-definition spatial transcriptomics with 2-μm resolution	Vickovic et al.

Molecular-based
2014	seqFISH	Allows the detection of transcripts at spatial level	Lubeck et Al.
2015	MERFISH	Multiplexed smFISH with error-robust barcodes	Chen et al.

Spatial MultiModal

Year	Title	Description	Reference
YYYY	10x Spatial Proteomics co-detection	Allows the co-detection of proteins and transcripts at spatial level	Ref
2020	High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue	detection of transcripts and proteins on a chip-placed tissue slice	Liu et al 2020

Others (if any)

Year	Title	Description	Reference
2021	Spatially mapped single-cell chromatin accessibility	spatial ATAC	Thornton et al. 2021

Spatial Omics Methods & Tools

This section is intended not only for papers, but also for packages, methods, approaches or guidelines for Spatial Omics data analysis and integration. Following subsection will be subsequently divided by argument while collecting them.

Spatial Transcriptomics Methods & Tools

Year	Title	Language	Description	Reference
2021	Giotto	R	Toolbox for integrative analysis and visualization of spatial expression data	Dries et al. 2021

Spatial Multi Modal Methods & Tools

Others (if any)

Year	Title	Language	Description	Reference
2020	MISTy	R	Multiview Intercellular SpaTial modeling framework for knowledge extraction and analysis of highly multiplexed, spatially resolved omics data.	Tanevski et al.