-
ITCR Monthly Teleconference September 4, 2015
07 Oct 2015 | Contributor(s): Juli Klemm
-
Brain Cancer Imaging Analytics
02 Oct 2015 | Presentations | Contributor(s): Christos Davatzikos
The transition of oncologic imaging from its “industrial era” to it is “information era” demands analytical methods that 1) extract information from this data that is clinically and biologically relevant; 2) integrate imaging, clinical, and genomic data via rigorous...
-
Trinity: RNA-Seq De novo Assembly Application
30 Jun 2015 | External Applications | Contributor(s): Grabherr MG, Brian Haas, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, Di Palma F, Birren BW, Nusbaum C, Lindblad-toh K, Friedman N, Regev A
Quick Guide for the ImpatientTrinity assembles transcript sequences from Illumina RNA-Seq data.Download Trinity here.Build Trinity by typing make : ; in the base installation directory.Assemble RNA-Seq data like so:Trinity --seqType fq --left reads_1.fq --right reads_2.fq...
-
CRAVAT - Cancer-Related Analysis of Variants Toolkit
23 Jun 2015 | External Applications | Contributor(s): Rachel Karchin, Michael C Ryan
cravat is a bioinformatics pipeline : ; that performs high-throughput cancer-related analysis of variants. it : ; utilizes three applications: CHASM (Cancer-Specific Analysis of Somatic Mutations), VEST and SVN-Get. More information on these tools is available at CHASM Software.Release...
-
Tools for Creation of Integrated Data Repository for Cancer Research
16 Jun 2015 | Presentations | Contributor(s): Guoqian Jiang
Admin Supplement Proposal Parent Projects: DeepPhe (PIs: Savova and Jacobson) caCDE-QA (PI: Jiang)
-
A Semantic Web-based Quality Assurance Tool for Cancer Study Common Data Elements
16 Jun 2015 | Presentations | Contributor(s): Guoqian Jiang
A poster presentation from the caCDE-QA project (PI: Jiang)
-
Notes from the ITCR Annual Meeting May 27-28, 2015
10 Jun 2015 | Downloads | Contributor(s): Ishwar Chandramouliswaran, Juli Klemm
Notes from the ITCR Annual Meeting May 27-28, 2015
-
UCSC Biomedical Evidence Graph Demonstration
03 Jun 2015 | Presentations | Contributor(s): Josh Stuart, ellrott
The BMEG demonstration includes the following elements: 1) Organization of crowd-source challenges to develop best-of-breed methods including an overview of current DREAM projects, living benchmarks; 2) Enabling cloud-ready methods for mass compute with examples of recently...
-
Seven Bridges Cancer Genomics Cloud Pilot TCGA 2015 symposium workshop presentation
23 May 2015 | Presentations | Contributor(s): Deniz Kural
Basic and translational cancer research creates the need to disseminate, manage, and interpret large heterogeneous datasets. The volume and complexity of the data now routinely generated by high-throughput technologies has become too costly for individual laboratories and many research...
-
Introduction to the Trinity Cancer Transcriptome Analysis Toolkit
05 Feb 2015 | Teaching Materials | Contributor(s): Brian Haas, Aviv Regev, Bill Barnett
This short video provides an overview of our ITCR-funded effort to leverage RNA-Seq and de novo transcriptome assembly to assist researchers in studying cancer transcriptomes. Visit our NCGAS Trinity/Galaxy portal to access these compute...
-
Video: Learn how TIES can help manage research resources
16 Jan 2015 | Presentations | Contributor(s): Girish Chavan, Rebecca Crowley
https://www.youtube.com/watch?v=EzjAo9LJ4tg
-
Report to the DICOM Standards Committee - December 4, 2015
10 Dec 2014 | Downloads | Contributor(s): Joseph Kalen
-
CRAVAT Introduction Video - Cancer Related Analysis of Variants
03 Dec 2014 | Teaching Materials | Contributor(s): Michael C Ryan
This video provides a brief overview of the CRAVAT web service(http://www.cravat.us/). CRAVAT provides annotation and analysis of cancer mutations. CRAVAT is free, very easy to use, and can handle large volumes of mutations.[[Youtube(xovmIy11Bcs)]]Please switch to 1080 resolution and watch...
-
CRAVAT Introduction Video - Cancer Related Analysis of Variants
03 Dec 2014 | Teaching Materials | Contributor(s): Michael C Ryan
This video provides a brief overview of the CRAVAT web service(http://www.cravat.us/). CRAVAT provides annotation and analysis of cancer mutations. CRAVAT is free, very easy to use, and can handle large volumes of mutations.[[Youtube(xovmIy11Bcs)]]Please switch to 1080 resolution and watch...
-
Analysis, integration and visualization of DNA methylation sequencing data
07 Nov 2014 | Presentations | Contributor(s): Maureen Sartor
Integrative epigenomic/genomic profiling and biomarker discovery of HPV+ and HPV- squamous cancers.
-
Summarization of Big Data
07 Nov 2014 | Presentations | Contributor(s): Jeffrey A. Blimes
All about assay selection...
-
Biomedical Evidence Graph
03 Oct 2014 | Presentations | Contributor(s): Josh Stuart
-
Tools to Analyze Morphology and Spatially Mapped Molecular Data
03 Oct 2014 | Presentations | Contributor(s): Joel Saltz
-
"DICOM 301" - Enhanced Multi-frame and Quantitation:
04 Sep 2014 | Presentations | Contributor(s): David Clunie
In-depth presentation on the Digital Imaging and Communications in Medicine StandardA one-hour presentation of DICOM presented by Dr. David Clunie for the members of DICOM Working Group 30, Small Animal Imaging.
-
pRainBow optical barcoding library
14 Aug 2014 | Reagents | Contributor(s): Andries Zijlstra
Note: this is a work in progress. About: pRainBow is a library of lentiviral vectors designed to allow for fluorescent labeling of cells with one of 7 distinct fluorescent proteins. Composition: How to obtain: How to cite: Other information:Good global...