User: morovatunc

gravatar for morovatunc
morovatunc360
Reputation:
360
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Trusted
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Turkey
Twitter:
mortunco
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4 days, 20 hours ago
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2 years ago
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Posts by morovatunc

<prev • 172 results • page 1 of 18 • next >
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Comment: C: Extract Cg Dinucleotides Coordinates From (Human) Genome
... I dont know if it useful or not but I used your script and it is running. Thank you. I have a question; What is the format that you got at the end of it. I had to put "End" manually but when I compared your chr,Start file format vs mine(chr start end gave the same thing. Thanks. ...
written 6 weeks ago by morovatunc360
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Comment: C: Regular Expression help for (bcf/vcf)tools filter manipulation
... Thank you very much. ...
written 6 weeks ago by morovatunc360
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How should I compare multiple TF methylation percentages?
... Hi, I would like to compare methylation percentage of multiple transcription factors. I have seen many differential methylation region analysis based on multiple samples but has any of you done this kind of analysis based on single sample and different subset of regions ? My aim is to score ever ...
encode methylation tf written 7 weeks ago by morovatunc360
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Regular Expression help for (bcf/vcf)tools filter manipulation
... Hi, I annotated the flanking regions of SNV mutations with vcftools fill-fs tool. In example; 20 10639675 . C G . . Callers=broad,dkfz,muse,sanger;NumCallers=4;VAF=0.3571;repeat_masker=L1M5;t_alt_count=25;t_ref_count=45;Variant_Classification=Intron;FS=t[C/G]c it added FS=t[C/G]c where; - ...
bcftools vcftools written 9 weeks ago by morovatunc360 • updated 9 weeks ago by Petr Ponomarenko2.4k
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Comment: C: 1000g database with wrong variant annotation?
... You can give it a try to ICGC or TCGA ? ( I see that you did not specify a sample type ). You just need to apply for the data. It contains bams, vcfs etc. ...
written 9 weeks ago by morovatunc360
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Answer: A: Does anybody success to download data using icgc-storage-client ?
... I have faced with the same problem before. I tried to download icgc data to my local from my local machine. Because all the data is stored in the amazon AWS cloud and you need to log-in to the AWS. Create an instance ( like a cloud machine ) and download icgc client overthere. Later on, you can use ...
written 10 weeks ago by morovatunc360
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Comment: C: Could you suggest me a proper feature selection method for mixed type variable d
... @Sirus thank you very much for your comment. The part where dividing data two train and test seems to confuse me a lot. Can only train my data ? and not do any prediction ?? Like a said in the question, i dont wan to predict anything. Is this possible with random forest? ...
written 12 weeks ago by morovatunc360
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Could you suggest me a proper feature selection method for mixed type variable data?
... Hi, We are working on cancer mutation data and we found that upon TF binding, there has been an enrichment of mutation occurrence happened on these TF binding regions. Since we couldnt a strong reason for this occurrence we wanted to use feature selection methods. We thought that say; Y ( mut ...
machine learning written 12 weeks ago by morovatunc360 • updated 11 weeks ago by cfay0
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Comment: C: Overlapping regions in a BedGraph file
... Hi, Is there any update about this post? Thanks. T. ...
written 3 months ago by morovatunc360
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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 3 months ago by morovatunc360

Latest awards to morovatunc

Popular Question 6 weeks ago, created a question with more than 1,000 views. For Chip-Seq Peak hight difference between BED and BW file formats.
Popular Question 3 months ago, created a question with more than 1,000 views. For HOMER find motifs from BED data
Popular Question 4 months ago, created a question with more than 1,000 views. For Kallisto New RNA-seq quantification method discussion
Popular Question 4 months ago, created a question with more than 1,000 views. For Visualization of Homer mergePeaks output Venn?
Voter 8 months ago, voted more than 100 times.
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Binding sites of annotated chip-seq peak files
Scholar 10 months ago, created an answer that has been accepted. For A: Binding sites of annotated chip-seq peak files
Popular Question 12 months ago, created a question with more than 1,000 views. For Kallisto New RNA-seq quantification method discussion
Centurion 13 months ago, created 100 posts.
Appreciated 15 months ago, created a post with more than 5 votes. For Kallisto New RNA-seq quantification method discussion
Supporter 20 months ago, voted at least 25 times.

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