User: hkarakurt
hkarakurt • 20
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- Joined:
- 1 year, 11 months ago
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- h********@gtu.edu.tr
Posts by hkarakurt
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... I am thinkg about my GTF file. The file I used in featureCounts step, includes genes and gene predictions (From USCD) and I used them for counting the MACS results. Is that make a big difference because I am not sure GTF file includes enhancers of genes. This is the point I am not sure about.
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written 10 months ago by
hkarakurt • 20
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... Sorry for late reply and thank you so much, I will look to csaw package.
But my question is; using only the DESeq2 (used featureCounts to have CountMatrix from with BAM files) is wrong?
Thank you.
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written 10 months ago by
hkarakurt • 20
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... Hello everyone,
I have a count matrix which has 5 different tissue types. I did differential gene expression analysis to them as 2 samples each time (the analysis I need actually) but I am planning to generate heatmap, clustering analysis, PCA and SOM to all samples so I need normalized counts for ...
written 11 months ago by
hkarakurt • 20
• updated
11 months ago by
Michael Love ♦ 22k
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... Hello everyone,
I need to do differential ChIP-Seq analysis to find the binding of genes between 2 conditions. I know there are lots of tools for that but I decided to use DESeq2 for that. I used MACS for peak calling and I had BAM files. Then used featureCounts to generate counts matrix. To this c ...
written 11 months ago by
hkarakurt • 20
• updated
11 months ago by
Michael Love ♦ 22k
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... I just checked and MS_getPathIds command is not working. It is in reference manual but R cannot find the function.
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written 12 months ago by
hkarakurt • 20
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... I will check the package.
Thank you so much.
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written 12 months ago by
hkarakurt • 20
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... Yes these are the data frames I want.
Actually format is not really important but mostly it should be a table which includes a column for gene and a column with associated compound.
Thank you for your answer.
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written 12 months ago by
hkarakurt • 20
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... Hello, I need to build a Gene-Metabolite (Compund) and Metabolite - Pathway network for Streptomyces coelicolor from KEGG. I tried KEGGREST package for R but I only can download Gene - Pathway network. Anyone knows how can I download this network with KEGGREST or any other packages?
Thank you,
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... Hello everyone,
I need to download whole protein-protein interaction network of Mus musculus. I downloaded from STRING but the file is too big to manipulate (about 12 million lines). I need to delete some interactions with low confidence score but I cannot open this file with Matlab, R, Python or E ...
written 12 months ago by
hkarakurt • 20
• updated
12 months ago by
damian.szk • 0
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... Hello everyone,
I want to do a differential coexpression analysis to a microarray data. My data have rows for genes and columns for conditions. 30 control and 28 disease columns.
I checked some packages such as WGCNA but I think they don't take expression data as input.
Anyone has any advice, tu ...
written 13 months ago by
hkarakurt • 20
• updated
13 months ago by
Peter Langfelder • 1.8k
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