User: Nicholas Spies

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Nicholas Spies1.1k
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United States, St. Louis, The Genome Institute at WUSTL
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NickSpies13
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5 years, 11 months ago
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Posts by Nicholas Spies

<prev • 7 results • page 1 of 1 • next >
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Comment: A: Machine Learning For Cancer Classification - Part 2 - Building A Random Forest C
... Thanks for the input! It's a great thought and I will add it to the example. ...
written 12 months ago by Nicholas Spies1.1k
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Comment: C: Machine Learning For Cancer Classification - Part 2 - Building A Random Forest C
... Hello,  The first three columns in the data set are non-numerical identifiers. We remove these to simplify the rest of the data-frame manipulations. Adding three to the index just makes sure gene order stays as intended. Hope this helps! Nick ...
written 4.1 years ago by Nicholas Spies1.1k
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Comment: C: How can I look at nonsense mutations in a particular gene in TCGA data?
... Yes, I absolutely agree. cBioPortal is a very powerful resource as well. Thanks for the suggestion and sorry for my oversight! ...
written 4.6 years ago by Nicholas Spies1.1k
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Answer: A: How can I look at nonsense mutations in a particular gene in TCGA data?
... If you are asking whether you can search for non-sense mutations between amino acids 2000-2500 of a particular gene in the TCGA sets, I would suggest using the Mutation Annotation Files (MAFs). These files have already been run through somatic variation calling so you won't have to deal with the seq ...
written 4.6 years ago by Nicholas Spies1.1k
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Cancer related Pathway Annotations
... Hello Everyone, I have recently become interested in analyzing mutation data for pathway enrichment. I have found GO terms to be incredibly noisy, and was wondering if anyone knew of a good Cancer-focused annotation set for genes implicated in cancer pathways. Thanks in advance!   Nick ...
pathway analysis cancer written 4.6 years ago by Nicholas Spies1.1k • updated 4.6 years ago by Siva1.6k
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Tutorial: Machine Learning For Cancer Classification - Part 4 - Plotting A Kaplan-Meier Curve For Survival Analysis
... This tutorial is part of a series illustrating basic concepts and techniques for machine learning in R. We will try to build a classifier of relapse in breast cancer. The analysis plan will follow the general pattern (simplified) of a recent paper. This follows from: Machine learning for cancer cla ...
R tutorial written 5.8 years ago by Nicholas Spies1.1k • updated 2.3 years ago by jmzeng131490
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Tutorial: Machine Learning For Prediction of Relapse in Cancer - Part 2 - Building A Random Forest Classifier
... This tutorial is part of a series illustrating basic concepts and techniques for machine learning in R. We will try to build a classifier of relapse in breast cancer. The analysis plan will follow the general pattern (simplified) of [a recent paper](http://www.ncbi.nlm.nih.gov/pubmed/24112773). Thi ...
R tutorial classification cancer written 5.8 years ago by Nicholas Spies1.1k • updated 12 months ago by RamRS24k

Latest awards to Nicholas Spies

Popular Question 3.7 years ago, created a question with more than 1,000 views. For Cancer related Pathway Annotations
Guru 3.7 years ago, received more than 100 upvotes.
Epic Question 4.5 years ago, created a question with more than 10,000 views. For Machine Learning For Cancer Classification - Part 2 - Building A Random Forest Classifier
Supporter 4.5 years ago, voted at least 25 times.
Scholar 4.6 years ago, created an answer that has been accepted. For A: How can I look at nonsense mutations in a particular gene in TCGA data?

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