User: hkarakurt
hkarakurt • 50
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Posts by hkarakurt
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... Thanks for your explanation and comment. ...
written 3 months ago by
hkarakurt • 50
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... I did not know it is a problem. I will try to delete my post here.
Thank you. ...
written 3 months ago by
hkarakurt • 50
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... 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 ...
written 3 months ago by
hkarakurt • 50
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... 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
hkarakurt • 50
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... 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
hkarakurt • 50
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... 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
hkarakurt • 50
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... 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 ...
written 3 months ago by
hkarakurt • 50
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... 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 ...
written 3 months ago by
hkarakurt • 50
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... I am looking for a R/Bioconductor package in fact but DAVID looks really nice also.
Thank you. ...
written 3 months ago by
hkarakurt • 50
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... 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 ...
written 3 months ago by
hkarakurt • 50
• updated
3 months ago by
caggtaagtat • 620
Latest awards to hkarakurt
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For Tool for predicting transcription factors from a gene list
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For Tool for predicting transcription factors from a gene list
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For Retrieving data from NCBI GEO and RNA-Seq Data Analysis
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14 months ago,
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For Retrieving data from NCBI GEO and RNA-Seq Data Analysis
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