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federicogiorgi / aracne.networks

aracne.networks, a data package containing gene regulatory networks assembled from TCGA data by the ARACNe algorithm
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Possible to obtain tcga datasets to make each regulon #1

Open saksham219 opened 6 years ago

saksham219 commented 6 years ago

Hi. I have been using aracne.networks to implement the VIPER algorithm. I was wondering if it would be possible to obtain a list of datasets/dataset for the regulons, specifically 'regulonpaad'. Something similar to what the package bcellViper provides (the regulon as well as the dset used to infer it). Thanks in advance.

federicogiorgi commented 6 years ago

Dear Saksham,

would you like to collaborate on your pancreas project? Concerning paad I have the raw counts dataset, the normalized dset but also many more data, e.g. mutation calls, miRNA expression, CNVs, and several processed analyses such as eQTL/aQTL. If you want, tell me more on what you will need specifically.

Best,

Federico

Federico M. Giorgi, PhD Senior Assistant Professor of Bioinformatics Dipartimento di Farmacia e Biotecnologie Università di Bologna Via Selmi 3 40100 Bologna Italy tel. +39 051 20 9 4227 cell. 339-4832494 federico.giorgi@unibo.it http://www.giorgilab.org https://www.unibo.it/sitoweb/federico.giorgi/en

On Fri, 28 Sep 2018 at 09:45, Saksham Malhotra notifications@github.com wrote:

Hi. I have been using aracne.networks to implement the VIPER algorithm. I was wondering if it would be possible to obtain a list of datasets/dataset for the regulons, specifically 'regulonpaad'. Something similar to what the package bcellViper provides (the regulon as well as the dset used to infer it). Thanks in advance.

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