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"ITCR Training Assets" 19 posts Sort by created date Sort by defined ordering View as a grid View as a list

Bioconductor help / training / outreach resources

Bioconductor home page and help material -- 'man' pages, vignettes, work flows, courses & conferences (including static resources), user support forum & devel mailing list, twitter, newsletter, community contributions, publications, etc. Introductory video.

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Martin Morgan onto ITCR Training Assets

TIES Training Resources

For institutional users (who deploy and customize SW):
Wiki-based documentation is at ties.pitt.edu (see Documentation and  also Features)

For end users:
Videos are available at local user-facing portals (e.g. ties.upmc.com/ and ties.upmc.com/radiology) 
A User Manual is also available.

 

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3D Slicer

3D Slicer is a multi-platform, free and open source software package for visualization and medical image computing. 3D Slicer pre-compiled application is freely available for Windows, Mac and Lunux. 3D Slicer is the main delivery platform for the ITCR QIICR project

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Cistrome Analysis Pipeline

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MeV

Description: MeV is a tool for genomic data analysis.

Code Repository

Authors, Institution: John Quackenbush, Dana-Farber Cancer Institute

 

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UCSC Xena Basic Tutorial

UCSC Xena is a tool that allows researchers and bioinformaticians to easily and securely view both their own cancer genomics data and data from large consortiums, such as TCGA, TARGET and GTEx. This video shows how to use Xena.

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UCSC Xena: Explain it to me!

UCSC Xena is a tool that allows researchers and bioinformaticians to easily and securely view both their own cancer genomics data and data from large consortiums, such as TCGA. This informational video explains Xena's functionality, helping you to decide if it is the right tool for you.

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NDEx - The Network Data Exchange

The NDEx Project provides an open-source framework where scientists and organizations can share, store, manipulate and publish biological network knowledge. The project maintains a Public NDEx Server and is a joint effort of the Cytoscape Consortium and the UC San Diego School of Medicine. Follow us on LinkedIn !!!

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TIES and the TIES Cancer Research Network

TIES is a natural language processing (NLP) pipeline and clinical document search engine that de-identifies, annotates, and indexes your clinical documents, making it easier to find and obtain data and biospecimens. TIES supports creation of federated networks for data and biospecimen sharing as part of The TIES Cancer Research Network.

 

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Apache cTAKES

Apache cTAKES is a natural language processing system for extraction of information from electronic medical record clinical free-text.

 

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Introduction to the Trinity Cancer Transcriptome Analysis Toolkit

The Trinity Cancer Transcriptome Analysis Toolkit aims to make available applications for studying cancer transcriptomes, including transcript reconstruction, identification of mutations, fusion transcripts, expression, and alternative splicing.   In a collaboration between the Broad Institute and Indiana University, we are making Trinity and cancer transcriptome targeted applications available to researchers via our Trinity/NCGAS Galaxy Portal.

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CRAVAT - Cancer-Related Analysis of Variants

CRAVAT is an easy to use web-based resource for annotation and scoring of genomic variants. CRAVAT is a cancer focused tool that assists researchers in filtering large sets of variant data, including indels, to identifying important mutations. 

Open video in HD

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MeV: Multiexperiment Viewer

MeV is a versatile microarray data analysis tool, incorporating sophisticated algorithms for clustering, visualization, classification, statistical analysis and biological theme discovery.

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Next-Generation Clustered Heat Maps (NG-CHM)

NG-CHM are highly interactive, dynamic clustered heatmaps that enable the user to see an overview of the entire heatmap, and via interactive navigation controls, to zoom and pan across the heatmap to see details of the heatmap at many levels of resolution.

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Tools to Analyze Morphology & Spatially Mapped Molecular Data

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QIICR: Quantitative Imaging Informatics for Cancer Research

Overview demonstration for the NCI ITCR QIICR project, http://qiicr.org presented on June 13, 2016 at the annual ITCR face-to-face meeting.

 

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NDEx - Video Demo - June 2016

This video demo was prduced for the Annual ITCR PI Meeting hosted by The Broad Institute in June 2016 and consists of 3 parts:

  • Part 1 describes several UI improvements for network search, including examples of advanced search features.
  • Part 2 introduces the new network visualizer that has been deployed to the NDEx Public server at the beginning of July 2016.
  • Finally, in part 3, we demonstrate a network round-trip between NDEx and Cytoscape that shows how layout and graphic style information are faithfully preserved.

For more information, please visit the NDEx Website and follow us on Twitter and LinkedIn

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GenePattern Notebook

The GenePattern Notebook environment gives GenePattern users the ability to interleave text, graphics and code with their GenePattern analyses to create "notebooks" that can be edited, shared and published. GenePattern Notebooks are built on the Jupyter Notebook system and extend it, allow researchers to embed the hundreds of analysis and machine learning methods in GenePattern within a notebook, without the need to write code.

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LesionTracker: Open-source extensible web viewer for oncology research and clinical trials

LesionTracker is an ITCR U24 funded project to create an open-source extensible imaging platform for measuring and longitudinally tracking lesions for oncology clinical trials and research.  The viewer runs in modern HTML5 compliant web-browsers.  We are working with several other ITCR project to integrate our viewer platform with other projects.  All source code as well as demos are available through the github site accessible through the Open Health Imaging Foundation (OHIF) website at www.ohif.org (OHIF is a non-profit 501c(3) foundation that supports open-source medical imaging techologies).

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