From ad115987babbe5165fb910db1ad5854f7ffb4044 Mon Sep 17 00:00:00 2001 From: Levi Waldron Date: Tue, 23 Aug 2022 11:14:18 +0200 Subject: [PATCH] links to other relevant code Also add to README.md --- README.md | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 4d47718..005399e 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,8 @@ # 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 @@ -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, @@ -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 @@ -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. + +###