User: hkarakurt

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hkarakurt100
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Posts by hkarakurt

<prev • 62 results • page 1 of 7 • next >
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Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
... 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 ...
scrna-seq batch correction rna-seq written 4 days ago by hkarakurt100
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Trimmomatic trims most of the reverse strand
... 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 ...
trimmomatic fastq trim bwa written 6 weeks ago by hkarakurt100 • updated 6 weeks ago by genomax92k
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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 3 months 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 3 months ago by hkarakurt100 • updated 3 months 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 4 months 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 4 months 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 4 months ago by hkarakurt100 • updated 4 months ago by Shalu Jhanwar470
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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 5 months ago by hkarakurt100 • updated 5 months ago by Kevin Blighe67k
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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 13 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 13 months ago by hkarakurt100

Latest awards to hkarakurt

Popular Question 6 weeks ago, created a question with more than 1,000 views. For Tool for predicting transcription factors from a gene list
Epic Question 11 weeks ago, created a question with more than 10,000 views. For Using Seurat 3 Data for Pseudotime Analysis in Monocle 3
Popular Question 3 months ago, created a question with more than 1,000 views. For Tool for predicting transcription factors from a gene list
Popular Question 4 months ago, created a question with more than 1,000 views. For Tool for predicting transcription factors from a gene list
Great Question 13 months ago, created a question with more than 5,000 views. For Using Seurat 3 Data for Pseudotime Analysis in Monocle 3
Great Question 13 months ago, created a question with more than 5,000 views. For Retrieving data from NCBI GEO and RNA-Seq Data Analysis
Popular Question 13 months ago, created a question with more than 1,000 views. For Tool for predicting transcription factors from a gene list
Popular Question 13 months ago, created a question with more than 1,000 views. For Mitochondrial Gene percentage threshold in single cell RNA-Seq
Popular Question 13 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 13 months ago, created a question with more than 1,000 views. For Cufflinks gives only CUFF names with a gtf.
Popular Question 13 months ago, created a question with more than 1,000 views. For Differential ChIP-Seq Analysis
Student 13 months ago, asked a question with at least 3 up-votes. For Mitochondrial Gene percentage threshold in single cell RNA-Seq
Supporter 14 months ago, voted at least 25 times.
Popular Question 16 months ago, created a question with more than 1,000 views. For Tool for predicting transcription factors from a gene list
Popular Question 16 months ago, created a question with more than 1,000 views. For How to extract expression data from RAW data.
Popular Question 16 months ago, created a question with more than 1,000 views. For Mitochondrial Gene percentage threshold in single cell RNA-Seq
Popular Question 16 months ago, created a question with more than 1,000 views. For Differential Coexpression Analysis
Student 17 months ago, asked a question with at least 3 up-votes. For Mitochondrial Gene percentage threshold in single cell RNA-Seq
Popular Question 20 months ago, created a question with more than 1,000 views. For Tool for predicting transcription factors from a gene list
Popular Question 20 months ago, created a question with more than 1,000 views. For Tool for predicting transcription factors from a gene list
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Tool for predicting transcription factors from a gene list
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
Popular Question 2.7 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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