User: CY

gravatar for CY
CY510
Reputation:
510
Status:
Trusted
Location:
United States
Website:
https://www.dna-ghost....
Last seen:
1 week, 6 days ago
Joined:
4 years, 9 months ago
Email:
c********@hotmail.com

Posts by CY

<prev • 262 results • page 1 of 27 • next >
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Did and why recent studies show superior predictive power using methylation data on early cancer detection
... There seems to be an increasing tend (in both academic and industry) of using methylation pattern for cancer detection / classification. It almost feels that methylation is superior on such task over other omics (somatic mutation or RNA expression). What I can think of this is: 1. Methylation data ...
cancer detection methylation written 4 weeks ago by CY510
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Example code of MCMC on somatic variant calling (site specific error model)
... Some advanced somatic variant calling algorithms use MCMC (something like [High-intensity sequencing reveals the sources of plasma circulating cell-free DNA variants][1]). I have already comprehend the statistical logic behind it after some learning process. I still need an example code to get an id ...
variant calling written 7 weeks ago by CY510
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Create synthetic data based on general description of molecular characteristic for modeling
... I have a modeling task that classifies cancer subtype based on several molecular features. However, I do not have raw data of tumor sample to extract these features. All I have are several published papers that relatively comprehensively describes these molecular characteristics of these cancer subt ...
next-gen written 3 months ago by CY510
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Comment: C: Why NB distribution is preferred in RNA-Seq while normal distribution is preferr
... From what I understanding, counting reads from RNA-Seq is like sampling reads aligned on specific gene from reads pool. It represents Poisson process where we have small p (probability) and large n (total reads). Plus we have biological variation between samples. Therefore, we got Poisson with large ...
written 3 months ago by CY510
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6 follow
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Why NB distribution is preferred in RNA-Seq while normal distribution is preferred in microarray?
... Most of DE tools (such as DE-Seq) applied in RNA-Seq assume that gene expression follows Negative Binomial distribution (because of both technical and biological variation). While DE tools originated from Microarray (such as limma) assumes normal distribution? Is this difference due to some technica ...
microarray rna-seq written 3 months ago by CY510
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Comment: C: Logit-normal distribution to model variation among biological replicates
... Thank you for replying. I can understand the binomial distribution part. What confused me is the logic of using logit-normal distribution to model between-replicates variation ...
written 4 months ago by CY510
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Logit-normal distribution to model variation among biological replicates
... I came across [rMATS][1] while doing research on differential alternative splicing (AS). It uses logit-normal distibution to model variation among biological replicates. I am having difficulty understanding the logics here. Can anyone share some insights on how logit-normal distribution can model ...
rmats distribution alternative splicing written 4 months ago by CY510 • updated 4 months ago by Kevin Blighe63k
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How does aligner determine strandness when doing alignment
... This is maybe a silly question. But I just realize that the FASTQ contains both DNA reads of both strand (forward and reverse). However when doing alignment, the strandness of each read is not provided. How does aligner determine the strandness of reads? I am sensing I missed something here. ...
alignment written 4 months ago by CY510
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Comment: C: Distinguishing real RNA-editing event from sequencing artifact due to reverse tr
... We can definited filter out SNP using matched genomic sequence. However, how does genomic sequence help us distinguish RT induced artifact from real editing events? such artifacts certainly can occur in RNA sample but not in genomic sample. ...
written 5 months ago by CY510
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Distinguishing real RNA-editing event from sequencing artifact due to reverse transcription
... It is known that reverse transcription during lib prep introduce relatively high amount of artifacts. In a typical RNA-editing analysis, how would we usually distinguish them from real editing events? ...
rna-editing sequencing artifact written 5 months ago by CY510

Latest awards to CY

Popular Question 8 weeks ago, created a question with more than 1,000 views. For what cause poly-G from NextSeq
Popular Question 11 weeks ago, created a question with more than 1,000 views. For what cause poly-G from NextSeq
Popular Question 4 months ago, created a question with more than 1,000 views. For what cause poly-G from NextSeq
Popular Question 4 months ago, created a question with more than 1,000 views. For Do multiple SNPs exist in same chromosome to be called allele?
Popular Question 4 months ago, created a question with more than 1,000 views. For what cause poly-G from NextSeq
Popular Question 5 months ago, created a question with more than 1,000 views. For what cause poly-G from NextSeq
Popular Question 7 months ago, created a question with more than 1,000 views. For what cause poly-G from NextSeq
Popular Question 8 months ago, created a question with more than 1,000 views. For what cause poly-G from NextSeq
Popular Question 8 months ago, created a question with more than 1,000 views. For what cause poly-G from NextSeq
Popular Question 8 months ago, created a question with more than 1,000 views. For what cause poly-G from NextSeq
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Popular Question 8 months ago, created a question with more than 1,000 views. For what cause poly-G from NextSeq
Popular Question 8 months ago, created a question with more than 1,000 views. For Any tools for predicting binding affinity between TCR and epitode?
Popular Question 9 months ago, created a question with more than 1,000 views. For what cause poly-G from NextSeq
Popular Question 10 months ago, created a question with more than 1,000 views. For what cause poly-G from NextSeq
Popular Question 10 months ago, created a question with more than 1,000 views. For Any tools for predicting binding affinity between TCR and epitode?
Popular Question 10 months ago, created a question with more than 1,000 views. For what cause poly-G from NextSeq
Popular Question 12 months ago, created a question with more than 1,000 views. For Detecting variants at very low fractions from ctDNA
Popular Question 13 months ago, created a question with more than 1,000 views. For Detecting variants at very low fractions from ctDNA
Great Question 13 months ago, created a question with more than 5,000 views. 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?
Popular Question 14 months ago, created a question with more than 1,000 views. For Detecting variants at very low fractions from ctDNA
Popular Question 20 months ago, created a question with more than 1,000 views. For what cause poly-G from NextSeq
Popular Question 20 months ago, created a question with more than 1,000 views. For why PCA for RNA-Seq but tSNE for scRNA-seq?
Prophet 20 months ago, created a post with more than 20 followers. For why PCA for RNA-Seq but tSNE for scRNA-seq?

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