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# GenomicSuperSignature
**Interpretation of RNA-seq experiments through robust, efficient comparison to public databases**

### PURPOSE

### Purpose
Thousands of RNA sequencing profiles have been deposited in public archives, yet
remain unused for the interpretation of most newly performed experiments. Methods
for leveraging these public resources have focused on the interpretation of existing
Expand All @@ -10,7 +11,7 @@ of new to existing experiments. The interpretability of common unsupervised anal
methods such as Principal Component Analysis would be enhanced by efficient comparison
of the results to previously published datasets.

### METHODS
### Methods
To help identify replicable and interpretable axes of variation in any given gene
expression dataset, we performed principal component analysis (PCA) on 536 studies
comprising 44,890 RNA sequencing profiles. Sufficiently similar loading vectors,
Expand All @@ -35,6 +36,8 @@ If you use GenomicSuperSignature in published research, please cite:
> *Nature Communications* **2022**;13: 3695.
> [doi: 10.1038/s41467-022-31411-3](https://www.nature.com/articles/s41467-022-31411-3)
### Other relevant code
The workflow to build the RAVmodel is available from https://github.com/shbrief/model_building which is archived in Zenodo with the identifier https://doi.org/10.5281/zenodo.6496552. All analyses presented in the GenomicSuperSignatures manuscript are reproducible using code accessible from https://github.com/shbrief/GenomicSuperSignaturePaper/ and archived in Zenodo with the identifier https://doi.org/10.5281/zenodo.6496612.

## Installation
You can install GenomicSuperSignature in Bioconductor. This can be done using
Expand Down Expand Up @@ -78,3 +81,5 @@ The GenomicSuperSignature package allows users to access a RAVmodel (Z matrix, b
GenomicSuperSignature connects different public databases and prior information through RAVindex, creating the knowledge graph illustrated here. Users can instantly access data and metadata resources from multiple entry points, such as gene expression profiles, MeSH terms, gene sets, and keywords.

<img src="https://raw.githubusercontent.com/shbrief/GenomicSuperSignaturePaper/master/inst/images/GSig_knowledge_graph.png" width="90%" height="90%"/>

###

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