User: Jordan Anaya

gravatar for Jordan Anaya
Jordan Anaya920
Reputation:
920
Status:
Trusted
Location:
US/Charlottesville
Website:
http://www.omnesres.com/
Last seen:
1 year ago
Joined:
2 years, 6 months ago
Email:
o**************@gmail.com

I perform open science at omnesres.com, where I blog, create tutorials, and share my work.  I also offer services to researchers and develop open access tools such as OncoLnc.

Posts by Jordan Anaya

<prev • 18 results • page 1 of 2 • next >
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Answer: A: PAN - TCGA survival analysis
... I'm not quite sure what type of plot you want to make. If you want to look at several genes in a single cancer I can understand that. For example, you can compare patients with high expression of both genes X and Y vs. low expression of both X and Y. To perform a pan-cancer Kaplan plot are you ju ...
written 22 months ago by Jordan Anaya920
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Comment: C: Guide to TCGA data
... Yeah, that link doesn't work anymore with the data portal no longer operational. I happened to copy that table to my blog a while back: http://www.omnesres.com/tools/tcga/ ...
written 2.1 years ago by Jordan Anaya920
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Comment: C: Link to TCGA mutation calling benchmark dead?
... I have no idea how to find previous TCGA files on the GDC portal. ...
written 2.1 years ago by Jordan Anaya920
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Answer: A: Link to TCGA mutation calling benchmark dead?
... They moved everything to the GDC: https://gdc.nci.nih.gov/, not sure if you'll be able to find what you're looking for. ...
written 2.1 years ago by Jordan Anaya920
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Comment: C: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
... When I look at correlations to survival with Firehose I find that they often list 0 genes correlating with survival. In contrast to their analysis, I have found thousands of genes that have significant p-values. ...
written 2.1 years ago by Jordan Anaya920
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Comment: C: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
... I program mainly in Python so I haven't tried running the code in this thread, but a patient vital status issue was raised recently for OncoLnc: https://github.com/OmnesRes/onco_lnc/issues/1 In this repository you will find Python code for extracting clinical data from files downloaded from the old ...
written 2.1 years ago by Jordan Anaya920
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Answer: A: Does TCGA have MLH1 gene methylation data?
... Have you tried using MEXPRESS? http://mexpress.be/ ...
written 2.2 years ago by Jordan Anaya920
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Answer: A: TCGA Methylation data is gone
... Yeah, I just learned about this change as well. I haven't taken a look at the files available at GDC yet, but I find this change to be very short sighted. There are numerous tools that rely upon the format of the files that were present at the old website and now these tools might be useless or ha ...
written 2.2 years ago by Jordan Anaya920
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Answer: A: Guide to TCGA data
... It has come to my attention that Tier 3 TCGA data has been moved from https://tcga-data.nci.nih.gov/tcga/ to https://gdc.nci.nih.gov/. ...
written 2.2 years ago by Jordan Anaya920
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Answer: A: Why there are genes that are not present in TCGA normalized rna-seq data?
... Yes, RNA-SEQ will give you the whole transcriptome, but you then have to take those reads and map them to transcripts. The transcript definitions used by the TCGA when they counted the reads determine how many genes will be in the normalized data from firebrowse. As a result, the transcripts from ...
written 2.4 years ago by Jordan Anaya920

Latest awards to Jordan Anaya

Epic Question 13 months ago, created a question with more than 10,000 views. For Guide to TCGA data
Popular Question 19 months ago, created a question with more than 1,000 views. For OncoLnc: A new TCGA data portal
Great Question 20 months ago, created a question with more than 5,000 views. For Guide to TCGA data
Gold Standard 21 months ago, created a post with more than 25 bookmarks. For Guide to TCGA data
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Guide to TCGA data
Scholar 2.4 years ago, created an answer that has been accepted. For A: Why there are genes that are not present in TCGA normalized rna-seq data?
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Why there are genes that are not present in TCGA normalized rna-seq data?
Librarian 2.5 years ago, created a post with more than 10 bookmarks. For Guide to TCGA data
Prophet 2.5 years ago, created a post with more than 20 followers. For Guide to TCGA data
Appreciated 2.6 years ago, created a post with more than 5 votes. For Guide to TCGA data
Autobiographer 2.6 years ago, has more than 80 characters in the information field of the user's profile.

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