User: hkarakurt
hkarakurt • 100
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Posts by hkarakurt
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... Hello everyone, First, I am so sorry if my post title does not correspond to my post completely.
I am using scater/scran package for scRNA-Seq analysis and MNN for batch correction.
As I know with multiple datasets; MNN integrates first and second datasets first and integrate the third one with fi ...
written 4 days ago by
hkarakurt • 100
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... Hello everyone,
I have a paired-end data. It is from small part of human genome not a WGS or WES. I use BWA for alignment and do variant calling. Since I had some false positives I wanted to do trimming.
I used trimmomatic with command:
trimmomatic PE -phred33 -threads 2 read1.fastq.gz read2.f ...
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... It was a hypothetical question. I meant if only one transcript of a gene have a SNP, how should I treat it? Is there any "main transcript annotation" of a gene or a scoring system. ...
written 3 months ago by
hkarakurt • 100
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... Hello,
I am doing WGS analysis and I have a question. As you know some genes have multiple transcripts in the genome. E.g. BRCA1 has about 30 transcripts.
As I understand one of the transcripts is enough to produce the related protein and transcription of the transcript is highly associated with tis ...
written 3 months ago by
hkarakurt • 100
• updated
3 months ago by
caggtaagtat • 1.3k
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... Thank you for your answer.
I am already using igraph but as I know it does not have a function to extract and analyze the subset of main graph.
I can try with a for loop. ...
written 4 months ago by
hkarakurt • 100
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... Thank you for your answer. I can use Cytoscape to analyze a subset of nodes but as I mentioned for more than 50 cluster (can go up to 350) it would be really time consuming activity. I am more like looking for a way to analyze each cluster with single function. ...
written 4 months ago by
hkarakurt • 100
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... Hello,
I have a really big PPI network and I clustered the network. Is there a way to analyze each cluster to find metrics of each cluster such as closeness, degree etc.
I want to treat each cluster as an independent network but I have 56 cluster so an automated library would be great.
I searched b ...
written 4 months ago by
hkarakurt • 100
• updated
4 months ago by
Shalu Jhanwar • 470
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... Hello everyone,
I need a transcription-factor gene network that has edge weights (or scores). I have networks from several databases but as I see regulatory networks are unweighted mostly.
Does anyone knows a weighted data set or any way to create weights?
Thank you in advance
...
written 5 months ago by
hkarakurt • 100
• updated
5 months ago by
Kevin Blighe ♦ 67k
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... Thank you so much for your answer. I tried your advice but there is a problem apparently.
When I use "design = model.matrix( ~ 0 + exp )" about 95% of the genes are signficantly changed and it looks wrong.
With my codes it was about 30%.
What is the disadvantage of using "~exp" instead of "~0 + ex ...
written 13 months ago by
hkarakurt • 100
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... Hello,
I have a microarray gene expression data set consists 30 samples for two groups (Wild Type and Mutant) with certain time points. I want to do differential expression analysis between conditions but I want my analyses to consider time points too. My data looks like this:
Sample Condition Time ...
written 13 months ago by
hkarakurt • 100
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