User: DVA

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DVA460
Reputation:
460
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Trusted
Location:
United States
Last seen:
3 days, 3 hours ago
Joined:
3 years, 10 months ago
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Posts by DVA

<prev • 141 results • page 1 of 15 • next >
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Extract the overlap of well-covered regions across multiple samples
... I am looking at somatic mutations across multiple samples, but the samples are not covered equally in many regions. Since we care about comparing the mutation counts between these samples, I would need to consider the uneven coverage -- e.g. sample A has 5X coverage at position 1, while sample B has ...
wgs coverage written 3 days ago by DVA460
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Comment: C: Pathway enrichment with differential expression p-values
... Thanks so much for the information! ...
written 4 weeks ago by DVA460
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Pathway enrichment with differential expression p-values
... Hello All, I have a large set of genes with differential expression p-values (from DEseq2) and directional (up or down-regulated) information. I was wondering if anyone knew of a pathway enrichment analysis program that could make use of all of this information rather than just the gene list? Sorry ...
gene enrichment written 4 weeks ago by DVA460 • updated 4 weeks ago by b.nota4.3k
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GSEA Phenotype Table Input
... Hello All, I am trying use GSEA for gene enrichment analysis, and I was wondering about the phenotype labels. Is there a way to test for the difference between two phenotypes while controlling for other phenotypes in a different category? For example, if I wanted to compare 5 cancer samples to 5 ...
gsea written 5 weeks ago by DVA460 • updated 4 weeks ago by c.chakraborty70
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Multiple factors & batch effects - DESeq2
... I have a question about how DEseq2 handles batch effects/ multiple factors. This is covered in the manual, but I just want to be certain I am doing it correctly. Say I have an experiment with this design: Sample Age Sex 1 Young F 2 Young F 3 Old F 4 Old F 5 Old F 6 Ol ...
deseq2 written 7 weeks ago by DVA460
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Comment: C: Horizontal lines in MA plot (DESeq2)
... Hi Kevin, Thank you for the reply. I think I kinda figured it out. Basically, it is described here: https://support.bioconductor.org/p/62927/ For every gene (row) DeSeq2 does a plus 1, to avoid 0 counts. Then it normalizes all samples based on the total count of each sample, and that gives a size ...
written 9 weeks ago by DVA460
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Horizontal lines in MA plot (DESeq2)
... Could someone help me understand why my MA plot from DEseq2 has this line of points close to zero, and a second line at about 1.2? I checked the genes from my count table corresponding to the points on these lines, and they have a very low read count in both samples. Thus I would really like to kn ...
deseq2 written 9 weeks ago by DVA460
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Comment: C: Which annotation file to use
... Thank you! This is very helpful! I'm trying to figure out a way to actually visualize what is going on. I will post the update soon. ...
written 11 weeks ago by DVA460
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Comment: C: High Unassigned Ambiguity in Feature Counts
... Hi Michael, thank you very much for all the help. I opened another post when I also realized the annotation files make a difference for my case. https://www.biostars.org/p/312498/#312744 However, as the discussion goes, there are more overlap with this post. I'm sorry about that. Nonetheless, thank ...
written 11 weeks ago by DVA460
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Comment: C: Which annotation file to use
... Thank you very much for looking into the details. I opened this new post when I was not sure why annotation file make a huge difference, and thought it would be a different/quick question. I apologize and I will also make a note in the previous post. I did tried both -s 2 and -s 1, and -s 2 gives ve ...
written 11 weeks ago by DVA460

Latest awards to DVA

Voter 4 months ago, voted more than 100 times.
Popular Question 6 months ago, created a question with more than 1,000 views. For Non-cancer somatic mutation calling
Popular Question 6 months ago, created a question with more than 1,000 views. For Output all allele counts at each position using bcftools
Popular Question 6 months ago, created a question with more than 1,000 views. For Manually edit the flags in a sam file
Popular Question 7 months ago, created a question with more than 1,000 views. For Non-cancer somatic mutation calling
Centurion 7 months ago, created 100 posts.
Popular Question 11 months ago, created a question with more than 1,000 views. For Non-cancer somatic mutation calling
Appreciated 11 months ago, created a post with more than 5 votes. For Develop an R package for CRAN vs BioConductor
Popular Question 11 months ago, created a question with more than 1,000 views. For Non-cancer somatic mutation calling
Popular Question 11 months ago, created a question with more than 1,000 views. For Remove both pair end reads with low mapping quality using Samtools
Popular Question 13 months ago, created a question with more than 1,000 views. For Remove both pair end reads with low mapping quality using Samtools
Student 16 months ago, asked a question with at least 3 up-votes. For Non-cancer somatic mutation calling
Popular Question 16 months ago, created a question with more than 1,000 views. For Remove both pair end reads with low mapping quality using Samtools
Appreciated 17 months ago, created a post with more than 5 votes. For Develop an R package for CRAN vs BioConductor
Good Question 17 months ago, asked a question that was upvoted at least 5 times. For Develop an R package for CRAN vs BioConductor
Student 18 months ago, asked a question with at least 3 up-votes. For Non-cancer somatic mutation calling
Popular Question 19 months ago, created a question with more than 1,000 views. For Identify point mutations from each read in sam files
Student 20 months ago, asked a question with at least 3 up-votes. For Non-cancer somatic mutation calling
Student 2.2 years ago, asked a question with at least 3 up-votes. For Non-cancer somatic mutation calling
Scholar 2.2 years ago, created an answer that has been accepted. For A: Can't locate dbSNP 131 anymore?
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Illumina's HiSeq strange Phred quality score
Scholar 2.4 years ago, created an answer that has been accepted. For A: Can't locate dbSNP 131 anymore?
Supporter 2.4 years ago, voted at least 25 times.
Scholar 2.4 years ago, created an answer that has been accepted. For A: Can't locate dbSNP 131 anymore?

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