User: mbk0asis

gravatar for mbk0asis
mbk0asis290
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Korea, Republic Of
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1 week, 2 days ago
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5 years, 9 months ago
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Posts by mbk0asis

<prev • 90 results • page 1 of 9 • next >
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Repetitive region expression in TCGA RNA-seq data?
... Hi, all! Does the TCGA RNA-seq dat contain the expression levels of repetitive regions (LINE, SINE, LTR, and etc.)? Thank you! ...
tcga repetitive regions written 6 weeks ago by mbk0asis290
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Answer: A: Subsetting DESeq2 results by padj quantity
... dta <- subset(result, padj<.1) dta_sorted = dta[order(dta$padj), ] write.table(head(dta_sorted,1000),"dta.tsv") ...
written 7 weeks ago by mbk0asis290
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Can we estimate actual copy number using Segment_means in TCGA level 3 CNV data?
... Hi, all! Can we estimate actual copy number using Segment_means in TCGA level 3 CNV data? If not, how to determine whether a gene is amplified or not? What is the typical threshold for the determination of "Gain/Loss" for TCGA data? Thank you! ...
tcga copy number cnv written 8 weeks ago by mbk0asis290
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Comment: C: plotProfile (deepTools) generated a peak on gene body region
... Your second suggestion sounds much easier, haha. Thank you! ...
written 9 weeks ago by mbk0asis290
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Comment: C: plotProfile (deepTools) generated a peak on gene body region
... I am stuck at the first step which is ID the outliers. I was going to export the matrix using "–outFileNameMatrix" option and edit the matrix. Then, how can I make the edited file back to the matrix file 'plotHeamap' recognizes? Should I just use other tools like R to draw the heatmap? ...
written 9 weeks ago by mbk0asis290
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Comment: C: plotProfile (deepTools) generated a peak on gene body region
... Thank you. I will give it a try. ...
written 10 weeks ago by mbk0asis290
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Comment: C: samtools rmdup error
... try again after converting the file into bam. ...
written 10 weeks ago by mbk0asis290
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plotProfile (deepTools) generated a peak on gene body region
... Hi, all! I'm trying to plot the DNA methylation profiles using deepTools and having annoying peaks on the gene body region as you can see the picture below. ![enter image description here][2] The code I used; $ computeMatrix scale-regions -S Sample1.bw Sample2.bw Sample3.bw -R genes.bed -a ...
plotprofile deeptools written 10 weeks ago by mbk0asis290 • updated 10 weeks ago by Devon Ryan76k
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Extraction of every n-th and m-th columns
... Hi. Everyone! I have a dataset similar to below. It has multiple samples, and each sample has multiple values. ID Sample1 Sample2 Sample3 xx val1 val2 va3 val4 val5 val1 val2 va3 val4 val5 val1 val2 va3 val4 val5 How can I extract multip ...
command bash written 3 months ago by mbk0asis290 • updated 3 months ago by Alex Reynolds22k
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Answer: A: TPM to logFC and pvalues
... Try to multiply by 100 or larger numbers to make them integers. ...
written 6 months ago by mbk0asis290

Latest awards to mbk0asis

Popular Question 5 weeks ago, created a question with more than 1,000 views. For overlapping texts (plot.PCA in FactoMineR)
Scholar 7 weeks ago, created an answer that has been accepted. For A: select DE genes
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Subsetting DESeq2 results by padj quantity
Student 5 months ago, asked a question with at least 3 up-votes. For Pairwise2 - Biopython - weird local alignment results
Popular Question 5 months ago, created a question with more than 1,000 views. For fasta - reverse complement sequence
Popular Question 7 months ago, created a question with more than 1,000 views. For fasta - reverse complement sequence
Scholar 7 months ago, created an answer that has been accepted. For A: select DE genes
Popular Question 11 months ago, created a question with more than 1,000 views. For Finding a sequence in a fasta file
Great Question 12 months ago, created a question with more than 5,000 views. For Finding a sequence in a fasta file
Popular Question 12 months ago, created a question with more than 1,000 views. For Finding a sequence in a fasta file
Popular Question 12 months ago, created a question with more than 1,000 views. For Finding a sequence in a fasta file
Popular Question 15 months ago, created a question with more than 1,000 views. For Finding a sequence in a fasta file
Popular Question 18 months ago, created a question with more than 1,000 views. For Pairwise2 - Biopython - weird local alignment results
Popular Question 24 months ago, created a question with more than 1,000 views. For Barcode (index) splitting
Supporter 2.0 years ago, voted at least 25 times.
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Finding a sequence in a fasta file

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