User: Assa Yeroslaviz

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Assa Yeroslaviz1.1k
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Munich
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http://www.biochem.mpg...
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AssaYeroslaviz
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6 years, 4 months ago
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I'm a bioinformatician in the bioinformatics group of the Max-Planck Institute for biochemistry in Munich, Germany. In our group we have a broad research focus that is mainly dedicated to help solving biological problems. We achieve this by a very close interaction with researchers in biological research labs, located here at the MPI-B in Munich, as well as in many other research institutions around the globe. Due to these close ties with a biological research environment, we are partly dedicating our efforts to the development of bioinformatics tools and databases that will help advance biological sciences.

Posts by Assa Yeroslaviz

<prev • 298 results • page 1 of 30 • next >
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Comment: C: calling objects from an embedded function
... Yes. I did, but it didn't help much. I have tried to understand how to correct it, but it seems, that everything I try keep briniging me to the same error message. What Am I doing wrong here? Do I need to define each time all the arguments needed in the nested function. meaning Should the call to ...
written 28 days ago by Assa Yeroslaviz1.1k
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calling objects from an embedded function
... I am trying to call for an object from a nested function. The object itself was created in the first (top) function. the function structure i am having is similar to this: top_function(input = input_file) { # hier I am reading in the data, converting it and modify the structure sampl ...
nested-function function object written 29 days ago by Assa Yeroslaviz1.1k
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Comment: C: Differential expression analysis of non-coding RNA-Seq data
... something like this featureCounts -T 15 -b -a Cel.WBcel235_subset.gtf -f -O -t exon -g transcript_id -o OUT.txt *.bam whereas the `Cel.WBcel235_subset.gtf` is the file containing only the rows from the original gtf file containing `ncRNA`. ...
written 6 weeks ago by Assa Yeroslaviz1.1k
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Comment: C: Differential expression analysis of non-coding RNA-Seq data
... This I did. In the first mapping run I have the complete gtf file containing all genes/transcripts including the `ncRNA` transcripts. How can I than do a DE analysis on the ncRNA transcripts? Or should I include them in the complete analysis? When I count the features for the total RNA-Seq using fe ...
written 6 weeks ago by Assa Yeroslaviz1.1k
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Comment: C: Differential expression analysis of non-coding RNA-Seq data
... Yes, I aligned only against the ncRNA with the file mentioned above. But I don't have a gtf file for it, so I was going to use the gtf file from the RNA-Seq analysis. But when I'm using the original gtf file all I can't seems to find any counts. The assigned reads when running featureCounts is 0% f ...
written 6 weeks ago by Assa Yeroslaviz1.1k
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Comment: C: Differential expression analysis of non-coding RNA-Seq data
... can I use the regular gtf file for the quantification of the counts? ...
written 6 weeks ago by Assa Yeroslaviz1.1k
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Differential expression analysis of non-coding RNA-Seq data
... Hi, I'm working on a data set from worm (*C. elegans*). I would like to analyse possible differential expression of ncRNA in the samples. I have five different conditions in triplicates. for the mapping I have doewloaded the data from Ensembl - [Caenorhabditis_elegans.WBcel235.ncrna.fa][1]. Af ...
deseq2 ncrna edger written 6 weeks ago by Assa Yeroslaviz1.1k
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Time series analysis from ChIP-Seq data
... Hi, I was wondering if there a way to run a time series analysis on ChIP-Seq data. We have duplicates of four different time points for two strains and three conditions. We have done IP, Input and IgG samples. Now I would like to identify differences over time comparing the different conditions w ...
time-series chip-seq time-course written 7 weeks ago by Assa Yeroslaviz1.1k • updated 14 days ago by geek_y8.1k
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Comment: C: geom_line with hclust data of expression matrix
... `bin` is a column and `cluster` in this case would be a row in the data.frame. I don't see how to combine these info together. ...
written 7 weeks ago by Assa Yeroslaviz1.1k
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Comment: C: geom_line with hclust data of expression matrix
... This doesn't work for me (AFAIK). The clusters are in a column. When I transpose the data to fit the structure I need, they will also become a row in the new matrix and I won't be able to melt them accordingly. Or do I miss something? ...
written 7 weeks ago by Assa Yeroslaviz1.1k

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