User: CY

gravatar for CY
CY350
Reputation:
350
Status:
Trusted
Location:
United States
Website:
https://www.dna-ghost....
Last seen:
8 hours ago
Joined:
3 years, 8 months ago
Email:
c********@hotmail.com

Posts by CY

<prev • 199 results • page 1 of 20 • next >
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Why so many biomarkers based classifiers claim high accuracy but rare used in clinical setting?
... This may not be technically related to bioinformatics. Using bioinformatics method, lots of biomarker (methylation; microRNA; mRNA; etc...) based classifiers (for benign / malignant tumor; tumor early detection; tumor subtype; etc) have been published and claim to have good performance. However, i ...
biomarker written 21 hours ago by CY350 • updated 20 hours ago by Kevin Blighe43k
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Mutated gene based pathway enrichment
... My goal is to find dysfunctioned pathways using mutated genes of hundred tumor samples as input. There are tools like GSEA that take expression data and perform pathway enrichment. I am wondering if there is similar enrichment tools that take mutated genes as input instead and perform enrichment a ...
enrichment mutation written 10 days ago by CY350 • updated 8 days ago by H.Hasani730
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Why seed and fuzzy-search in MIGEC?
... I was playing around with test data of MISEG (for the purpose of analyzing TCR data with UMI). The barcode.txt records the adaptor sequence + UMI (marked as N). The adapter sequences is either lower or upper cased indicating fuzzy or seed search according to the manual. I am curious about the port ...
migec mui tcr written 5 weeks ago by CY350
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Comment: C: Why can't use t-test for differential expression (negative binomial distribution
... I have read it. It is very straightforward and heapful. ...
written 7 weeks ago by CY350
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Comment: C: Why can't use t-test for differential expression (negative binomial distribution
... It is pure academic interest. Want to get a rough picture of how DE is done. ...
written 7 weeks ago by CY350
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Comment: C: Why can't use t-test for differential expression (negative binomial distribution
... Do you have any reference about this n > 20? ...
written 7 weeks ago by CY350
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Comment: C: Why can't use t-test for differential expression (negative binomial distribution
... I just want to get a rough picture of how DE is tested in general. ...
written 7 weeks ago by CY350
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Comment: C: Why can't use t-test for differential expression (negative binomial distribution
... If I first normlize the raw counts the way most DE tools normalize it taking account of library size, heteroscedasticity, etc. Can I use t-test on these normalized counts if sample size is sufficient? ...
written 7 weeks ago by CY350
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Comment: C: Why can't use t-test for differential expression (negative binomial distribution
... Even though counts don't approach normal distribution, central limit theorem still allow me to use t-test on normalized counts if we have sufficient sample size (although most like we don't), right? ...
written 7 weeks ago by CY350
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Comment: C: Why can't use t-test for differential expression (negative binomial distribution
... By "if I have large number of sample", is it because that gene expression follows non-normal distribution (although follows a similar one). Only with large number of samples would the expression statistics converge to normal distribution (by central limit theorem). Am I understand it correctly? ...
written 7 weeks ago by CY350

Latest awards to CY

Popular Question 11 days ago, created a question with more than 1,000 views. For Detecting variants at very low fractions from ctDNA
Popular Question 6 months ago, created a question with more than 1,000 views. For what cause poly-G from NextSeq
Popular Question 6 months ago, created a question with more than 1,000 views. For why PCA for RNA-Seq but tSNE for scRNA-seq?
Prophet 6 months ago, created a post with more than 20 followers. For why PCA for RNA-Seq but tSNE for scRNA-seq?
Popular Question 8 months ago, created a question with more than 1,000 views. For why PCA for RNA-Seq but tSNE for scRNA-seq?
Popular Question 8 months ago, created a question with more than 1,000 views. For STAR genomeLoad issue
Popular Question 9 months ago, created a question with more than 1,000 views. For why PCA for RNA-Seq but tSNE for scRNA-seq?
Appreciated 11 months ago, created a post with more than 5 votes. For why PCA for RNA-Seq but tSNE for scRNA-seq?
Good Question 11 months ago, asked a question that was upvoted at least 5 times. For why PCA for RNA-Seq but tSNE for scRNA-seq?
Student 13 months ago, asked a question with at least 3 up-votes. For why PCA for RNA-Seq but tSNE for scRNA-seq?
Centurion 15 months ago, created 100 posts.
Supporter 18 months ago, voted at least 25 times.
Popular Question 19 months ago, created a question with more than 1,000 views. For Call variant from RNA-Seq data using Haplotypecaller

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