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Forum: General 11-22-2014, 04:11 AM
Replies: 3
Views: 2,814
Posted By GenePool
We've put together a resource which allows one to...

We've put together a resource which allows one to query for over-expression and amplification in Cancer genomics samples, particularly those profiled by The Cancer Genome Atlas.

Here are some...
Forum: General 11-22-2014, 04:09 AM
Replies: 8
Views: 3,726
Posted By GenePool
Here are a few threads on a tool we've put...

Here are a few threads on a tool we've put together to help explore cancer genomics data, particularly The Cancer Genome Atlas:

http://seqanswers.com/forums/showthread.php?t=42471...
Forum: RNA Sequencing 11-22-2014, 03:50 AM
Replies: 2
Views: 4,212
Posted By GenePool
If you look at the "DESCRIPTION.TXT" files...

If you look at the "DESCRIPTION.TXT" files included in each package, there is the following description:

This data archive contains the miRNA expression data for cancer samples
of The Cancer...
Forum: Bioinformatics 11-22-2014, 03:32 AM
Replies: 7
Views: 26,090
Posted By GenePool
Hi, Yep, as Benjamin has pointed out, we...

Hi,

Yep, as Benjamin has pointed out, we have found the data in the *.normalized_results to be the most robust and comparable across samples and experiments. We've also done some testing against...
Forum: Bioinformatics 11-22-2014, 03:25 AM
Replies: 2
Views: 2,450
Posted By GenePool
Hi, Yep, like Richard has pointed out, you...

Hi,

Yep, like Richard has pointed out, you need to get a hold of analysis IDs.

We typically use https://browser.cghub.ucsc.edu/ to search for the samples that we're interested in, and then...
Forum: Bioinformatics 11-22-2014, 03:16 AM
Replies: 4
Views: 2,464
Posted By GenePool
Hi Mous, We've put this data into GenePool...

Hi Mous,

We've put this data into GenePool and much of the RNA-Seq data is freely available to the community. We've linked all of the genomics data (such as RNA-Seq) to the relevant patient &...
Forum: Bioinformatics 11-22-2014, 03:12 AM
Replies: 1
Views: 2,973
Posted By GenePool
Hi, We have made the Breast Cancer microRNA...

Hi,

We have made the Breast Cancer microRNA level 3 data freely available as part of a free preview of GenePool's premium content. This data is prepped and ready to analyze in GenePool.
...
Forum: Vendor Forum 11-22-2014, 12:15 AM
Replies: 1
Views: 4,453
Posted By GenePool
The Cancer Genome Atlas (TCGA) comprehensively available in GenePool

Station X (http://www.stationxinc.com/) has recently made The Cancer Genome Atlas comprehensively available instantly for users of GenePool.

GenePool now provides instant access to the following...
Forum: Vendor Forum 11-22-2014, 12:12 AM
Replies: 0
Views: 5,237
Posted By GenePool
The Cancer Genome Atlas (TCGA) available in GenePool

GenePool is Station X (http://www.stationxinc.com/)’s software environment for the management, analysis and sharing of cohort-scale genomics data. GenePool makes it easy for translational and...
Forum: Vendor Forum 04-15-2014, 04:16 PM
Replies: 1
Views: 4,453
Posted By GenePool
Free Genomics Data Reference Library for the Community

In order to accelerate our understanding of the molecular basis of diseases such as cancer, it is imperative for the research community to be able to work with large cohorts of patient-derived...
Forum: General 03-27-2014, 03:59 PM
Replies: 15
Views: 2,996
Posted By GenePool
Hi, you might want to check out GenePool as a...

Hi, you might want to check out GenePool as a resource for supporting genomics education. It is built with a very intuitive interface that makes working with genomics fairly approachable for students...
Forum: Bioinformatics 03-27-2014, 11:21 AM
Replies: 2
Views: 2,100
Posted By GenePool
Hi All, We've included TCGA gene-level read...

Hi All,

We've included TCGA gene-level read counts as part of freely available reference library of genomics data in our product, GenePool. These counts were generated using the RNASeqV2 pipeline...
Forum: Bioinformatics 03-27-2014, 11:17 AM
Replies: 4
Views: 10,066
Posted By GenePool
Hi All, For what it's worth, we're committed...

Hi All,

For what it's worth, we're committed to making this sort of data more freely available and usable by the community. In that spirt, we've included a freely available reference library of...
Forum: RNA Sequencing 03-27-2014, 11:08 AM
Replies: 3
Views: 1,670
Posted By GenePool
Hello! You might want to check out the...

Hello!

You might want to check out the genomics reference library that is freely available in GenePool. It is a growing resource that we're making freely available to the community, and it...
Forum: Bioinformatics 03-27-2014, 11:03 AM
Replies: 2
Views: 2,108
Posted By GenePool
Hi, There are actually adjacent normals...

Hi,

There are actually adjacent normals available for a subset of patients per cohort that were profiled by RNA-Seq, while the DNA sequence variation data (genomes, exomes) is generated from...
Forum: Bioinformatics 03-27-2014, 10:56 AM
Replies: 1
Views: 1,414
Posted By GenePool
Hi, If you're interested in working with...

Hi,

If you're interested in working with TCGA expression data, you might be interested in checking out the free genomics reference library that Station X has recently launched as part of GenePool....
Forum: Bioinformatics 03-27-2014, 10:51 AM
Replies: 1
Views: 1,763
Posted By GenePool
Hi Matthew, We at Station X totally feel...

Hi Matthew,

We at Station X totally feel that TCGA data needs to be more freely accessible and approachable by the research community. In that spirit, we've recently launched a free reference...
Forum: General 03-27-2014, 10:45 AM
Replies: 1
Views: 2,472
Posted By GenePool
Hi Shahenda, Yes there are a number of...

Hi Shahenda,

Yes there are a number of normal-adjacent samples available for the RNA-Seq. In fact, you can freely browse and analyze the RNA-SeqV2 (level 3) gene-level data in GenePool by taking...
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