User: morovatunc

gravatar for morovatunc
morovatunc310
Reputation:
310
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Trusted
Location:
Turkey
Twitter:
mortunco
Last seen:
an hour ago
Joined:
1 year, 9 months ago
Email:
m*********@gmail.com

Posts by morovatunc

<prev • 164 results • page 1 of 17 • next >
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Comment: C: Overlapping regions in a BedGraph file
... Hi, Is there any update about this post? Thanks. T. ...
written 4 days ago by morovatunc310
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Comment: C: pheatmap vs. manual hclust with different results
... you are not scaling your data when you do hclust(dist(data)). But in pheatmap, you scale your data based on column ? In pheatmap help section it says it uses hclust therefore, I think your error was caused by not giving the same input. pheatmap also have distance matrix output so check; 1) if your ...
written 7 days ago by morovatunc310
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Comment: C: Somatic variant call
... Have you tried giving a chance to ensemble mutation calling ? I am using ICGC cancer data for my project and I clearly see that merging passed could be very stringent. They have their own pipeline for getting a consensus from multiple callers. - 1) https://github.com/bioinform/somaticseq —> take ...
written 7 days ago by morovatunc310
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Transcription Factor Specific Mutation Signature Enrichment
... Hi, I am analyzing TF proximity mutations in ICGC cancer cohort and I would like to prove that upon TF binding mutation signature profile changes. When I analysed TF proximity mutation with mutations signature analysis packages (such as SomaticSignature). It gives the "the famous" signature graph ...
R mutation signature written 14 days ago by morovatunc310
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Comment: C: TCGA UUIDS to TCGA barcode (SampleID) in R
... Thank you. It worked for my prostate cancer RNA-seq data. ...
written 18 days ago by morovatunc310
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Comment: C: about Mapability and Blacklisted regions?
... Thank you very much. ...
written 25 days ago by morovatunc310
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Comment: C: Varriant Annotation-exporting results
... I was trying to say are you sure about that directory is existing but I made a typo. Anyways, first of all this is not a regular R data frame. It is called Granges object. ( https://www.bioconductor.org/packages/devel/bioc/vignettes/GenomicRanges/inst/doc/GenomicRangesIntroduction.pdf —> check fo ...
written 25 days ago by morovatunc310
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Comment: C: Varriant Annotation-exporting results
... Could you show a sample from your data ? Also are you about the given location ` G:/mydata.txt` is existing ? ...
written 25 days ago by morovatunc310
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about Mapability and Blacklisted regions?
... HI, I am using a GEO dataset which contains couple ChIP-seq peak files. (BEDs). To eleminate false discovery and low quality data, I would like to filter black listed regions (by DAC and Duke) and low mapability regions. I have couple questions related to this process. 1) For mapability which k-me ...
mapability ucsc written 25 days ago by morovatunc310 • updated 25 days ago by Devon Ryan64k
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Proving spesific TF binding locations have mutation enrichment than rest of the binding sites statistically
... We are analyzing cancer patient mutation data. We defined set of region on the human genome as binding events, and would like to prove that some of the region have significantly higher number of mutations than others. To prove this, we decided to set a mutation number threshold to say, there is at l ...
stat chip-seq written 28 days ago by morovatunc310

Latest awards to morovatunc

Popular Question 4 weeks ago, created a question with more than 1,000 views. For HOMER find motifs from BED data
Popular Question 7 weeks ago, created a question with more than 1,000 views. For Kallisto New RNA-seq quantification method discussion
Popular Question 8 weeks ago, created a question with more than 1,000 views. For Visualization of Homer mergePeaks output Venn?
Voter 6 months ago, voted more than 100 times.
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Binding sites of annotated chip-seq peak files
Scholar 8 months ago, created an answer that has been accepted. For A: Binding sites of annotated chip-seq peak files
Popular Question 9 months ago, created a question with more than 1,000 views. For Kallisto New RNA-seq quantification method discussion
Centurion 10 months ago, created 100 posts.
Appreciated 12 months ago, created a post with more than 5 votes. For Kallisto New RNA-seq quantification method discussion
Supporter 17 months ago, voted at least 25 times.

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