Projects

You have access to these projects within The Genboree Commons:

Project	Description
Allelic_Epigenome	Project contains annotation file required for processing files as described on the GitHub page
Epigenome_Informatics_Workshop	This project contains sub-projects for each Epigenome Informatics Workshop starting in 2012.
6th Workshop - March 2013	This project contains information and documents related to the 6th Epigenome Informatics Workshop held in Houston in March 2013, and organized by the Bioinformatics Research Laboratory (BRL) at the Baylor College of Medicine. The workshop focused on using tools within the Genboree Workbench. The BRL wishes to acknowledge the NIH Epigenomics Roadmap Project for its generous support of this workshop....
ASHG Workshop - Oct 2013	This project contains information and documents related to the American Society of Human Genetics (ASHG) Workshop held in Boston in October 2013. The workshop was organized by the Bioinformatics Research Laboratory (BRL) at the Baylor College of Medicine. The workshop, titled "Human Epigenome Atlas and Epigenomic Profile Analysis Using the Genboree Workbench" focused on analysis using various tools within the Genboree Workbench. The BRL wishes to acknowledge the NIH Epigenomics Roadmap Project for its generous support of this workshop. ...
Epigenomic Deconvolution	This page contains all the material associated with the publication named: "Epigenomic Deconvolution reveals association between stromal composition and metabolic phonotype of breast tumors". You will find scripts and datasets associated with that publication in the Documents tab....
exRNA Data Coordination Center	This project contains information about the Data Coordination Center (DCC) of the exRNA Communication Consortium. This figure gives an overview of the DMRR infrastructure. ...
All Dataset Submissions	This subproject keeps track of the different submissions that have been deposited into the Atlas as well as those submissions that are currently awaiting processing.
<Private Project>	You do not have access to this project, but you may have access to some sub-projects within.
Other Documents
Relevant Literature (Eugene)
Relevant Literature (Michael)
Public	This Public Genboree Commons Project contains information pertaining to the Genboree Commons and Genboree Workbench (getting started, Workbench icons, FAQs, etc.).
<Private Project>	You do not have access to this project, but you may have access to some sub-projects within.
Amin V et al Nat Comm 2015
Transcriptome Toolset	This project contains tutorials, use cases, workshop materials for Transcriptome toolset in the Genboree workbench
exRNA Tools	This project contains tutorial materials for the extracellular RNA data analysis tools available on Genboree. Introduction to Processing Your exRNA Samples Using the Genboree Workbench...
MIBlood-EV (ISEV)	MIBlood-EV: Minimal Information to Enhance the Quality and Reproducibility of Blood Extracellular Vesicle Research Blood is the most commonly used body fluid for extracellular vesicle (EV) research. The composition of a blood sample and its derivatives (i.e., plasma and serum) are not only donor-dependent but also influenced by collection and preparation protocols. Since there are hundreds of pre-analytical protocols and over forty variables, the development of standard operating procedures for EV research is very challenging. To improve the reproducibility of blood EV research, the International Society for Extracellular Vesicles (ISEV) Blood EV Task Force proposes standardized reporting of (i) the applied blood collection and preparation protocol and (ii) the composition of the prepared plasma and serum samples. Gathering detailed information provides insight into the performance of the protocols and in the presence of confounders in the prepared plasma and serum samples. To collect this information, the ISEV Blood EV Task Force created the Minimal Information for Blood EV research (MIBlood-EV), a tool to record and report information about pre-analytical protocols used for plasma and serum preparation as well as assays used to assess the quality of these preparations. This tool can be easily implemented in existing databases allowing for future meta-analysis and followed by evidence-based optimization of pre-analytical protocols. Taken together, insight into the quality of prepared plasma and serum samples will (i) improve the quality of biobanks for EV research, (ii) allow the exchange of plasma and serum samples between biobanks and laboratories, (iii) facilitate comparative EV studies, (iv) improve the peer review process, and, finally (v) does not require modifications of local pre-analytical protocols....

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