User: hkarakurt

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hkarakurt100
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Posts by hkarakurt

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Comment: C: SNPs on a single transcript of a gene with multiple transcripts
... 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 5 weeks ago by hkarakurt100
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SNPs on a single transcript of a gene with multiple transcripts
... 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 ...
gene wgs wes snp written 5 weeks ago by hkarakurt100 • updated 5 weeks ago by caggtaagtat1.3k
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Comment: C: Network Analysis of Each Cluster of Protein Interaction Network
... 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 8 weeks ago by hkarakurt100
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Comment: C: Network Analysis of Each Cluster of Protein Interaction Network
... 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 8 weeks ago by hkarakurt100
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Network Analysis of Each Cluster of Protein Interaction Network
... 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 ...
R network ppi python written 8 weeks ago by hkarakurt100 • updated 8 weeks ago by Shalu Jhanwar460
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Weighted gene regulatory networks
... 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 ...
network chip-seq regulatory written 3 months ago by hkarakurt100 • updated 3 months ago by Kevin Blighe65k
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Comment: C: Differential Expression Analysis of Two Groups Time Series Data with Limma
... 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 11 months ago by hkarakurt100
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Differential Expression Analysis of Two Groups Time Series Data with Limma
... 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 ...
microarray limma rna-seq differential expression written 11 months ago by hkarakurt100
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Comment: C: Using FPKM and TPM values for batch correction for Single Cell RNA-Seq
... They are completely different data sets from same biological sample ...
written 11 months ago by hkarakurt100
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Comment: C: Using FPKM and TPM values for batch correction for Single Cell RNA-Seq
... I am planning to check tximport package to convert FPKM and TPM values to counts. I found the function. I think you mean that one. ...
written 11 months ago by hkarakurt100

Latest awards to hkarakurt

Popular Question 5 weeks ago, created a question with more than 1,000 views. For Tool for predicting transcription factors from a gene list
Popular Question 8 weeks ago, created a question with more than 1,000 views. For Tool for predicting transcription factors from a gene list
Great Question 11 months ago, created a question with more than 5,000 views. For Using Seurat 3 Data for Pseudotime Analysis in Monocle 3
Great Question 11 months ago, created a question with more than 5,000 views. For Retrieving data from NCBI GEO and RNA-Seq Data Analysis
Popular Question 11 months ago, created a question with more than 1,000 views. For Tool for predicting transcription factors from a gene list
Popular Question 11 months ago, created a question with more than 1,000 views. For Mitochondrial Gene percentage threshold in single cell RNA-Seq
Popular Question 11 months ago, created a question with more than 1,000 views. For How to extrach gene names and peaks from BedGraph or BigWig files
Popular Question 11 months ago, created a question with more than 1,000 views. For Cufflinks gives only CUFF names with a gtf.
Popular Question 11 months ago, created a question with more than 1,000 views. For Differential ChIP-Seq Analysis
Student 11 months ago, asked a question with at least 3 up-votes. For Mitochondrial Gene percentage threshold in single cell RNA-Seq
Supporter 11 months ago, voted at least 25 times.
Popular Question 14 months ago, created a question with more than 1,000 views. For Tool for predicting transcription factors from a gene list
Popular Question 14 months ago, created a question with more than 1,000 views. For How to extract expression data from RAW data.
Popular Question 14 months ago, created a question with more than 1,000 views. For Mitochondrial Gene percentage threshold in single cell RNA-Seq
Popular Question 14 months ago, created a question with more than 1,000 views. For Differential Coexpression Analysis
Student 14 months ago, asked a question with at least 3 up-votes. For Mitochondrial Gene percentage threshold in single cell RNA-Seq
Popular Question 17 months ago, created a question with more than 1,000 views. For Tool for predicting transcription factors from a gene list
Popular Question 18 months ago, created a question with more than 1,000 views. For Tool for predicting transcription factors from a gene list
Popular Question 23 months ago, created a question with more than 1,000 views. For Tool for predicting transcription factors from a gene list
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Retrieving data from NCBI GEO and RNA-Seq Data Analysis
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Retrieving data from NCBI GEO and RNA-Seq Data Analysis

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