User: hkarakurt

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hkarakurt10
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Posts by hkarakurt

<prev • 14 results • page 1 of 2 • next >
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Comment: C: Differential ChIP-Seq Analysis with DESeq2
... 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. ...
written 5 weeks ago by hkarakurt10
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Comment: C: Differential ChIP-Seq Analysis with DESeq2
... 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. ...
written 6 weeks ago by hkarakurt10
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Normalized Values of Multi Sample Count Matrix with DESeq2
... 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 ...
rnaseq normalization deseq2 written 7 weeks ago by hkarakurt10 • updated 7 weeks ago by Michael Love18k
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Differential ChIP-Seq Analysis with DESeq2
... 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 ...
chipseq deseq2 featurecounts differential binding analysis written 8 weeks ago by hkarakurt10 • updated 8 weeks ago by Michael Love18k
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Comment: C: Gene-Metabolite and Metabolite-Pathway network from KEGG with KEGGREST
... I just checked and MS_getPathIds command is not working. It is in reference manual but R cannot find the function. ...
written 3 months ago by hkarakurt10
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Comment: C: Gene-Metabolite and Metabolite-Pathway network from KEGG with KEGGREST
... I will check the package. Thank you so much. ...
written 3 months ago by hkarakurt10
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Comment: C: Gene-Metabolite and Metabolite-Pathway network from KEGG with KEGGREST
... 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. ...
written 3 months ago by hkarakurt10
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Gene-Metabolite and Metabolite-Pathway network from KEGG with KEGGREST
... 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, ...
keggrest kegg written 3 months ago by hkarakurt10 • updated 3 months ago by 7kemZmani10
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How to download All Protein Protein Interactions of an organism with Bioconductor
... 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 ...
mus musculus stringdb ppi written 3 months ago by hkarakurt10 • updated 3 months ago by damian.szk0
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Differential Coexpression Analysis
... 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 ...
differential gene expression correlation coexpression differential analysis written 4 months ago by hkarakurt10 • updated 4 months ago by Peter Langfelder1.5k

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