opennano

Name	opennano JSON
Version	0.1.2 JSON
	download
home_page	https://github.com/Niamhck/opennano
Summary	A Python package for processing NanoString GeoMx data.
upload_time	2024-12-15 14:37:14
maintainer	None
docs_url	None
author	Charalampos Anagnostakis, Laura Beltrame, Cristiano Cordì, and Niamh Callian Keenan
requires_python	>=3.10
license	MIT
keywords	nanostring geomx spatial transcriptomics bioinformatics
VCS
bugtrack_url
requirements	No requirements were recorded.
Travis-CI	No Travis.
coveralls test coverage	No coveralls.

            <div align="center">
   <img src="OpenNano.png",
   height=300>
</div>

## Open Nano

Open Nano is a free open-source python package developed to address a lack of Python-based tools for analyzing Nanostring GeoMx DSP data.

From your dcc, pkc, and metadata files, you can:
-  create an AnnData object of your data 
-  perform quality control and normalization steps
-  do a differential gene expression analysis
-  look at spatial autocorrelation with Moran's I statistic
-  perform UMAP and tSNE clustering

Benchmarked against GeoMxTools R package and DESeq2.

See 

Created by Charalampos Anagnostakis, Laura Beltrame, Cristiano Cordì, and Niamh Callian Keenan
as part of the Integrated Bioinformatics Project for the MSc in Bioinformatics at KU Leuven, Belgium

            

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