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cran / MetaIntegrator

:exclamation: This is a read-only mirror of the CRAN R package repository. MetaIntegrator — Meta-Analysis of Gene Expression Data. Homepage: http://biorxiv.org/content/early/2016/08/25/071514
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Data availability for MetaSignature (Haynes et al, 2017)? #4

Open dhimmel opened 3 years ago

dhimmel commented 3 years ago

Note I am aware this repo is a read-only mirror on the CRAN source code and is not maintained by the authors. Nonetheless, it does appear to be most appropriate public venue for questions related to MetaSignature. I will email the authors to alert them to my question.

Greetings, I'm interested in the differential expression signatures of disease at https://metasignature.stanford.edu/ and described in:

Empowering multi-cohort gene expression analysis to increase reproducibility
Winston A Haynes, Francesco Vallania, Charles Liu, Erika Bongen, Aurelie Tomczak, Marta Andres-Terrè, Shane Lofgren, Andrew Tam, Cole A Deisseroth, Matthew D Li, … Purvesh Khatri
Pacific Symposium on Biocomputing (2017) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5167529/
DOI: 10.1142/9789813207813_0015 · PMID: 27896970 · PMCID: PMC5167529 · bioRxiv: 071514v1

The interface for interactive browsing at https://metasignature.stanford.edu/ is nice, and I'm interested in exploring the underlying data further.

Are the following datasets available?

  1. The datasets used to compute diffex signatures for each disease, for example a GEO dataset ID to disease mapping.
  2. The manual case-control assignments within experiments
  3. Diffex statistics for all disease-gene pairs (on the website I only see how to show top results).
gaborcsardi commented 3 years ago

Hi, this is a read only mirror of CRAN, please see the package authors and possibly URLs in the DESCRIPTION file. Thanks!

dhimmel commented 3 years ago

Thanks @gaborcsardi for the heads up. I'm aware (see preamble of my initial comment). I emailed metasignature-developers@lists.stanford.edu to alert the MetaSignature / MetaIntegrator team to my question. Hopefully we can keep further discussion here.