vjcitn
commented
7 years ago Levi, I'll try to function as a scribe.
On Sun, Oct 22, 2017 at 12:26 AM, Levi Waldron notifications@github.com wrote:
This SIG will discuss recent and needed Bioconductor data classes. Some recent or in-testing data classes to discuss are:
- MultiAssayExperiment (for "gluing" different types of assays together)
- RaggedExperiment (for copy number, mutations, or other data represented by different genomic ranges for each sample)
- restfulSE::RESTfulSummarizedExperiment, restfulSE:: BQSummarizedExperiment for remote storage + local interactive analysis of very large datasets
One presently identified need is a Bioconductor class for representing the drug sensitivity data from pharmacogenomics studies. Such studies, such as the Cancer Cell Line Encyclopedia (CCLE) and NCI-60, perform standard -omics assays, but also dose-response experiments where cell lines are subjected to varying doses of each of numerous compounds, and the responses are measured as cell viability. The resulting dose-response curves are then summarized using measures such as LC-50. The PharmacoGx https://bioconductor.org/packages/PharmacoGx/ Bioconductor package from the @bhaibeka https://github.com/bhaibeka lab provides numerous curated pharmacogenomics datasets as rich PharmacoSet objects, but these lack the flexibility and novel data storage models that would be available using a SummarizedExperiment-derived object for sensitivity data contained along with -omics assays within a MultiAssayExperiment. Therefore a desired outcome from this SIG is a draft class definition for cell line drug sensitivity data extending from SummarizedExperiment. This would accomplish both a needed new data class, and experience for those participating in extending existing core data structures to novel data types.
Topic leader: Levi Waldron @lwaldron https://github.com/lwaldron Scribe: Vincent Carey @vjcitn https://github.com/vjcitn (Vince can I volunteer you?)
Any interested participants are invited to use the issue to ask questions, suggest other relevant topics for discussion, and/or express their interest in participating.
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bhaibeka
p-smirnov
lgatto
lwaldron
lawremi
federicomarini
This SIG will discuss recent and needed Bioconductor data classes. Some recent or in-testing data classes to discuss are:
MultiAssayExperiment(for "gluing" different types of assays together)RaggedExperiment(for copy number, mutations, or other data represented by different genomic ranges for each sample)restfulSE::RESTfulSummarizedExperiment,restfulSE::BQSummarizedExperimentfor remote storage + local interactive analysis of very large datasetsOne presently identified need is a Bioconductor class for representing the drug sensitivity data from pharmacogenomics studies such as the Cancer Cell Line Encyclopedia (CCLE) and NCI-60. These studies perform standard -omics assays, but also dose-response experiments where cell lines are subjected to varying doses of each of numerous compounds. Responses are measured as cell viability, and the resulting dose-response curves are summarized using measures such as LC-50. The full dose-response data are a 3-D array (dose x time x cell line), which should be stored in addition to summary measure matrices (e.g. LC-50 concentration x cell line) The PharmacoGx Bioconductor package from the @bhaibeka lab provides numerous curated pharmacogenomics datasets as rich
PharmacoSetobjects, but these lack the flexibility and novel data storage models that would be available using aSummarizedExperiment-derived object for sensitivity data contained along with -omics assays within aMultiAssayExperiment. Therefore a desired outcome from this SIG is a draft class definition for cell line drug sensitivity data extending fromSummarizedExperiment. This would accomplish both a needed new data class, and experience for those participating in extending existing core data structures to novel data types.Topic leader: Levi Waldron @lwaldron Scribe: Vincent Carey @vjcitn (Vince can I volunteer you?)
Any interested participants are invited to use the issue to ask questions, suggest other relevant topics for discussion, and/or express their interest in participating.