Posts Tagged ‘bioinformatics’

Pacbio MCF-7 transscriptome dataset

Wednesday, July 30th, 2014

BLOG:
http://blog.pacificbiosciences.com/2013/12/data-release-human-mcf-7-transcriptome.html

DATASETS:
http://datasets.pacb.com.s3.amazonaws.com/2013/IsoSeqHumanMCF7Transcriptome/list.html

PAWG-WGL Links for PCAWG upload status

Friday, July 4th, 2014

PanCancer.info has fantastic #viz of the progress & int’l effort in the Pan-#Cancer Analysis of Whole #Genomes (#PCAWG) project

DREAM mutation calling challenge

Saturday, June 7th, 2014

Deadlines: 7/19,8/2,8/16
https://www.synapse.org/#!Synapse:syn312572

Broad Institute’s Firehose Dashboard

Monday, March 17th, 2014

Contains information on analysis pipelines and datasets produced from Broad’s Firehose. Access to the protected pages requires an NCI login.

https://confluence.broadinstitute.org/display/GDAC/Home

BioLayout

Saturday, January 4th, 2014

QT:{{”
BioLayout Express3D has been specifically designed for visualization, clustering, exploration and analysis of very large network graphs in two- and three-dimensional space derived primarily, but not
exclusively, from biological data.
“}}
www.biolayout.org

HuRef sperm sequencing

Saturday, January 4th, 2014

http://genome.cshlp.org/content/early/2013/01/02/gr.144600.112.abstract

huref on Solid

Saturday, January 4th, 2014

QT:{{”
To demonstrate the promise of personalized genome analysis, the genome of HuRef was sequenced using the Life SOLiDâ„¢ platform. Nimbus Informatics performed the analytical work for this project and has made the resulting data available here, running entirely on the Amazon Cloud.
“}}
http://huref.nimbusinformatics.com

BETASEQ: A Powerful Novel Method to Control Type-I Error Inflation in Partially Sequenced Data for Rare Variant Association Testing

Monday, December 23rd, 2013

http://bioinformatics.oxfordjournals.org/content/early/2013/12/12/bioinformatics.btt719.short

Genomics Researchers Imagine their Ideal Computer

Monday, December 9th, 2013

http://chronicle.com/article/Still-Hunting-Medical/143221/

Paul Basken
The Chronicle of Higher Education

CCLE WGS dataset

Monday, December 9th, 2013

This is the URL for ccle with WGS data:

https://cghub.ucsc.edu/datasets/ccle.html

They have an XML describe all the datasets and there are WGS as well. (This should be publicly available WGS.)

QT:{{”

The Cancer Cell Line Encyclopedia (CCLE) project is a collaboration between the Broad Institute, the Novartis Institutes for Biomedical Research, and the Genomics Institute of the Novartis Research Foundation. CCLE will conduct a detailed genetic and pharmacologic characterization of a large panel of human cancer models, develop an integrated computational analyses that link distinct pharmacologic vulnerabilities to genomic patterns and translate cell line
integrative genomics into cancer patient stratification. The CCLE provides public access to genomic data, analysis and visualization for about 1000 cell lines.

NOTE: these data sets do NOT require any special access or authorization status. However, you will need to use the public access token/key URL, or your secure key file that you may have downloaded for projects like TCGA that use a secure key file.

“}}