User: daniele.avancini

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Posts by daniele.avancini

<prev • 15 results • page 1 of 2 • next >
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Comment: C: Subset multiple columns in R or unix
... Can you transpose the data frame and extract the resulting rows? t_mydata<-t(mydata) geneList <- read.table("your_geneList.txt") subsampled_mydata <- t_mydata[which( t_mydata$Gene %in% geneList),] supposing there is a column Gene in your new t_mydata data frame ...
written 15 months ago by daniele.avancini60
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Comment: C: How to find differentially expressed genes between three groups?
... My apologies, I did not know you could and thank for pointing it out. Could you elaborate a bit more on how to convert categories into numeric scores? Anyway, I said that it was not possible because I thought you needed a fold change and the significance of that fold change in order to get to any c ...
written 15 months ago by daniele.avancini60
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Answer: A: How to find differentially expressed genes between three groups?
... Using classic tools (Deseq2, edger.. ) is not possible, they usually allow the comparison between two groups at a time. And rightly so, in my humble opinion since its the nature of differential expression which has only two dimensions (up or downregulated). However, you can use some tricks such as ...
written 15 months ago by daniele.avancini60
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Answer: A: Correlation matrix between enhancers and promoters (human)?
... I've spoken directly to the curators of the FANTOM5 database and they directed me to the source of the file. To whom it may concern, this is the link to enhancer-promoter correlation matrix I was talking about: [http://slidebase.binf.ku.dk/human_enhancers/presets][1] [1]: http://slidebase.binf. ...
written 17 months ago by daniele.avancini60
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Comment: C: Correlation matrix between enhancers and promoters (human)?
... Thanks, @geek_y. That was one of the paper I took information from but it wasn't the source of my file. ...
written 17 months ago by daniele.avancini60
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Correlation matrix between enhancers and promoters (human)?
... Dear all, I need your help in finding a file I downloaded while ago but I cannot find anymore online. The file is a correlation matrix between enhancer and promoters calculated as described in An atlas of active enhancers across human cell types and tissues (Andersson et al, 2014). The file is co ...
enhacer promoters correlation cage written 17 months ago by daniele.avancini60
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Diffbind for ATAC-seq data with no controls
... Hi all, I'm trying to use Diffbind to identify differentially open regions (identified using ATAC-seq) between three different cell types. I have three biological replicates for each cell type. I'm building now the sample sheet to import the data into Diffbind, but I don't know what I should indica ...
diffbind atac-seq written 2.1 years ago by daniele.avancini60 • updated 2.1 years ago by Rory Stark680
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Comment: C: Mitochondrial contamination over 90% in published atac-seq dataset.
... Thanks ATPoint for sharing with me your script, I'll definitely use that in the future. I did no calculation, to be honest, I just filtered the bam file for chrM tags and I was left with less than 10% of the mapped reads. Still don't know what I'm doing wrong with those files, don't know if is a map ...
written 2.4 years ago by daniele.avancini60
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Comment: C: Mitochondrial contamination over 90% in published atac-seq dataset.
... The new analysis using bowtie instead of bowtie2 gave a bit better results with an average MT mapping around 80%. Still high, but is the best I could get and I don't really know where I find this discrepancy in the data. I will call the peaks anyway and see what happens. Do you have any further sug ...
written 2.6 years ago by daniele.avancini60
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Comment: C: Mitochondrial contamination over 90% in published atac-seq dataset.
... Thank again, I will post the results of the new analysis. ...
written 2.6 years ago by daniele.avancini60

Latest awards to daniele.avancini

Scholar 17 months ago, created an answer that has been accepted. For A: Correlation matrix between enhancers and promoters (human)?
Popular Question 22 months ago, created a question with more than 1,000 views. For Huge difference between differential peaks with EdgeR and DESeq2 using Diffbind
Popular Question 22 months ago, created a question with more than 1,000 views. For Mitochondrial contamination over 90% in published atac-seq dataset.

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