User: hkarakurt

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hkarakurt50
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Posts by hkarakurt

<prev • 43 results • page 1 of 5 • next >
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Comment: C: Dunn Index for Clusters from scRNA-Seq
... Thanks for your explanation and comment. ...
written 3 months ago by hkarakurt50
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Comment: C: Dunn Index for Clusters from scRNA-Seq
... I did not know it is a problem. I will try to delete my post here. Thank you. ...
written 3 months ago by hkarakurt50
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Dunn Index for Clusters from scRNA-Seq
... Hello everyone, I want to try Dunn Index to validate my clustering results from scRNA-Seq data. I know the Dunn index starts from 0 and goes to infinity and higher results mean better clustering. I tried this method from scRNA-Seq which clustered with buildSNNGraph() function of Scater/Scran package ...
scrna-seq scater clustering dunn index scran written 3 months ago by hkarakurt50
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Comment: C: Differential Expression Analysis between conditions of single cell RNA-Seq
... Actually my data is just like Damian pointed out. I have 4 data sets for each condition and they are from 2 different batches. ...
written 3 months ago by hkarakurt50
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Comment: C: Differential Expression Analysis between conditions of single cell RNA-Seq
... Thank you for your answer. I will read the article. In fact, I identified my clusters. I did it seperately for my 2 data sets (different conditions) and you are right I am interested in the effect of condition change on a subset. I did not used CCA method of Seurat, I build my pipeline on Scater pac ...
written 3 months ago by hkarakurt50
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Comment: C: Differential Expression Analysis between conditions of single cell RNA-Seq
... I have real batch effect. I have 2 data sets for 2 conditions. Their experimental methods, platforms and tissues are same only conditions are different. I identified the cell types of clusters in data sets seperately now I want to compare specific cell types between conditions. ...
written 3 months ago by hkarakurt50
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Differential Expression Analysis between conditions of single cell RNA-Seq
... Hello everyone, I am working on scRNA-Seq data analysis and I have a technical question. We can combine different scRNA-Seq experiments with batch correction methods such as MNN or CCA. As I know, while doing differential expression analysis we should consider batch effect like Scater/Scran package ...
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Mitochondrial Gene percentage threshold in single cell RNA-Seq
... Hello everyone, I am working on scRNA-Seq data analysis. As most of you know high mitochondrial gene percentage indicates low quality (damaged or dead cells etc.) and we need to filter that. Is this threshold for identify the low quality cell data dependent? Because for each data set we see a diffe ...
scrna-seq rna-seq mitochondrial genes written 3 months ago by hkarakurt50
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Comment: C: Enrichment Analysis with only GeneSymbols
... I am looking for a R/Bioconductor package in fact but DAVID looks really nice also. Thank you. ...
written 3 months ago by hkarakurt50
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Enrichment Analysis with only GeneSymbols
... Hello everyone, I was looking to other posts but could not find a proper answer. I have a list of significantly changed genes and I want to do enrichment analysis with them. Is there a R/Bioconductor package that does this analysis with only GeneSymbols. Most of the packages require other informatio ...
scrna-seq enrichment rna-seq R written 3 months ago by hkarakurt50 • updated 3 months ago by caggtaagtat620

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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 8 months ago, created a question with more than 1,000 views. For Tool for predicting transcription factors from a gene list
Popular Question 12 months ago, created a question with more than 1,000 views. For Retrieving data from NCBI GEO and RNA-Seq Data Analysis
Popular Question 14 months 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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