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awesome-spatial-omics

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# awesome-spatial-omics [![Awesome](https://awesome.re/badge-flat2.svg)](https://awesome.re)

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](https://github.com/drighelli/awesome-spatial-omics/blob/main/CONTRIBUTING.md) 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](https://github.com/seandavi/awesome-single-cell) and the [Sean Davis' Awesome Single Cell](https://github.com/mikelove/awesome-multi-omics) 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](https://www.10xgenomics.com/products/spatial-gene-expression)|Allows the detection of transcripts at spatial spot level| [Ståhl et al.](https://science.sciencemag.org/content/353/6294/78.long)|  
|2019|HDST|High-definition spatial transcriptomics with 2-μm resolution|[Vickovic et al.](https://www.nature.com/articles/s41592-019-0548-y)|

|Molecular-based||||
|:-|:-|:-|:-|
|2014|[seqFISH](https://www.seqfish.com/technology)|Allows the detection of transcripts at spatial level| [Lubeck et Al.](https://www.nature.com/articles/nmeth.2892) |
|2015|[MERFISH](http://zhuang.harvard.edu/merfish.html)|Multiplexed smFISH with error-robust barcodes| [Chen et al.](https://science.sciencemag.org/content/348/6233/aaa6090) |

## 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 Multi Modal Methods & Tools

### Others (if any)
|Year|Title|Language|Description|Reference|
|:-:|:--|:-:|:--|:--|
|2020| [MISTy](https://saezlab.github.io/misty/)| R |Multiview Intercellular SpaTial modeling framework for knowledge extraction and analysis of highly multiplexed, spatially resolved omics data.|[Tanevski et al.](https://www.biorxiv.org/content/10.1101/2020.05.08.084145v1.full.pdf)

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