User: Assa Yeroslaviz

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Assa Yeroslaviz1.4k
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Munich, Germany
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Posts by Assa Yeroslaviz

<prev • 280 results • page 2 of 28 • next >
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Comment: C: How do I extract the complete MsaAAMultipleAlignment object to a file
... Hi, Yes I am sure. I have solved it by adding the parameter halfNrow = 100 ...
written 5 months ago by Assa Yeroslaviz1.4k
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Comment: C: How do I extract the complete MsaAAMultipleAlignment object to a file
... Sorry i was happy too fast. this is not exactly what I need. When I do this, I still get only the first nine row and the lst nine rows of the file with the ... between them. I would like to get the complete file - in my case all 154 rows in the text file. Is this possible? ...
written 5 months ago by Assa Yeroslaviz1.4k
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Comment: C: How do I extract the complete MsaAAMultipleAlignment object to a file
... thanks, but this is not exactly what I need ...
written 5 months ago by Assa Yeroslaviz1.4k
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Comment: C: How do I extract the complete MsaAAMultipleAlignment object to a file
... Thanks for the answer. It would be great if you can make it happens for BioC 3.8.  But if clustal is not possible, is there a way to extract the object `as is` ? I have this results object:  MsaAAMultipleAlignment with 154 rows and 1142 columns aln (1..79) ...
written 5 months ago by Assa Yeroslaviz1.4k
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How do I extract the complete MsaAAMultipleAlignment object to a file
... Hi all, I was wondering how I can export the results of my `msa` run into a file. I know I can export it to a fasta file using `unmasked(msa)`, but I would like to export the complete results I see in the terminal to a file or if possible in clustal format.  this is my script: P <- msa(seqs, ...
export msa msaprettyprint() multiplealignment written 5 months ago by Assa Yeroslaviz1.4k • updated 5 months ago by UBodenhofer250
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Comment: C: complex design for chip-seq analysis
... Thanks for the answer and the reference. But I am not sure, what you mean by that. How can I ignore the Input file, after running a peak caller. I did use MACS2 to call for peaks. But how do I get the counts per Gene/Transcript/TSS after running a peak caller? I know I can get the counts from a ba ...
written 8 months ago by Assa Yeroslaviz1.4k
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Comment: C: complex design for chip-seq analysis
... Thanks Aaron for the really elaborate answer. So if I understand it correctly, it is ok to use edgeR (and for that case also DESeq) with ChIP-Seq data? I thought it was meant only for RNA-Seq, as the reads are Poisson distributed and not negative binomial. Am I wrong with this assumption? Another d ...
written 8 months ago by Assa Yeroslaviz1.4k
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resize functions causes an error - "could not find function "unsafe.update"
... When running the resize function, I keep getting the following error message: > tAE <- IRanges::resize(tA, 200, fix = "center") Error in unsafe.update(object, ...) : could not find function "unsafe.update"   I have read that this might happens when you have older packages conflicted wi ...
iranges genomicranges resize written 8 months ago by Assa Yeroslaviz1.4k
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complex design for chip-seq analysis
... I have a chip-seq data set with three conditions (wt , KO1, KO2) and three time points (0h, 2h, 4h). For each condition and TP I have duplicated samples for IP and Input samples, which looks like that: condition TP Replicate IP Input wt 0h 1 IP Input ...
chipseq limma multiple factor design design matrix csaw written 8 months ago by Assa Yeroslaviz1.4k • updated 8 months ago by Aaron Lun20k
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pheatmap - Error in do_one(nmeth) : NA/NaN/Inf in foreign function call (arg 1)
... I am trying to plot a heatmap using pheatmap().  I'm using the following script to set the parameters and plot the various clusters.  hmx.parameters <- list(counts_filtered_df, color = col.pal, cellwidth = 15, cellheight = 12, scale = "none", treeheight_row = 200, kmeans_k = ...
kmeans pheatmap written 8 months ago by Assa Yeroslaviz1.4k

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