User: Assa Yeroslaviz

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Assa Yeroslaviz1.3k
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AssaYeroslaviz
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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 • 433 results • page 1 of 44 • next >
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Comment: C: Converting scRNA-Seq to Bulk-RNASeq
... thanks. After searching for the term "Pseudo bulk" I found more information. But it seems to me that as António mentioned above it all relates to calculating DE between clusters. What we would like to do though is a differential expression analysis on the complete data set. We are encountering the ...
written 2 days ago by Assa Yeroslaviz1.3k
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Converting scRNA-Seq to Bulk-RNASeq
... for the initial analysis of our data set we would like to convert our single-cell RNA-Seq into Bulk RNA-Seq by summarizing the #reads per gene per sample. I was wondering if anyone has already some experience with this kind of analysis. Would it make sense to calculate the average expression for ...
single-cell bulk-rnaseq scrnaseq rna-seq written 2 days ago by Assa Yeroslaviz1.3k
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subsetting seurat object with multiple samples
... I have a seurat object with 10 samples (5 in duplicates). I have added them all together and created the `VlnPlot` to check for the quality of the samples. As one can see in the pic below, the quality is quite different in each of the duplicated conditions. I was wondering, if it make more sense to ...
scrna-seq seurat written 16 days ago by Assa Yeroslaviz1.3k • updated 16 days ago by jared.andrews076.2k
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Comment: C: Error in Heatmap creation with RnBeads
... ok, thanks, The heatmaps via `meth()` and `heatmap.` I already managed for some. To make the hatmaps one must make sure, that the matrix contains only `complete.cases()`, as `heatmap.2` can't handle `NaN`. For the "sites" data I get the error - `Error: cannot allocate vector of size 2974245.6 Gb ...
written 6 weeks ago by Assa Yeroslaviz1.3k
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Comment: C: Error in Heatmap creation with RnBeads
... Good Morning, another thing I can't understand is that the run was done without errors, when running the whole pipeline with the `rnb.run.analysis` command, so why does it causes problems now? ...
written 6 weeks ago by Assa Yeroslaviz1.3k
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Comment: C: Error in Heatmap creation with RnBeads
... So let's say I would like to have the heatmaps. what command do I use? Or Can I only do it within R? ...
written 6 weeks ago by Assa Yeroslaviz1.3k
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Comment: C: Error in Heatmap creation with RnBeads
... Hi again, I'm not sure, but it looks strange to me. When I run the separate commands for the clustering it works fine. > clusterings.sites <- rnb.execute.clustering(rnb.set, region.type="sites") 2020-06-02 15:24:12 12.1 STATUS Performed clustering on sites using correlation as a ...
written 6 weeks ago by Assa Yeroslaviz1.3k
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Comment: C: Error in Heatmap creation with RnBeads
... Thanks for the fast response I don't think this is a RAM problem $free -h total used free shared buff/cache available Mem: 1.0T 23G 325G 3.0G 659G 980G Swap: 0B 0B 0B I'l ...
written 6 weeks ago by Assa Yeroslaviz1.3k
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Error in Heatmap creation with RnBeads
... When running the exploratory data analysis step (`rnb.run.exploratory`) I get an error message in the heatmap creation step 2020-06-02 03:26:26 62.5 STATUS COMPLETED Agglomerative Hierarchical Clustering 2020-06-02 03:26:29 62.5 STATUS STARTED Clustering Sect ...
bs-seq rnbeads written 6 weeks ago by Assa Yeroslaviz1.3k • updated 6 weeks ago by mscherer50
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What sequence do I get when using paired-end stranded protocol
... I know this is a very basic question, but I tend to mix them always. I was wondering what reads Do I get at the end, when I run a paired-end directional (or stranded) library preparation protocol. I know from [here][1], that in a single-end directional protocol the reads I see in the fastq files ar ...
directional paired-end stranded rna-seq sequencing written 6 weeks ago by Assa Yeroslaviz1.3k • updated 6 weeks ago by caggtaagtat1.1k

Latest awards to Assa Yeroslaviz

Great Question 8 weeks ago, created a question with more than 5,000 views. For estimation of size factors in DESeq2 analysis
Popular Question 4 months ago, created a question with more than 1,000 views. For HOWTO extract regions from GRanges object
Popular Question 4 months ago, created a question with more than 1,000 views. For fastqc Exception in thread "Thread-1" (error)
Popular Question 4 months ago, created a question with more than 1,000 views. For HOWTO extract regions from GRanges object
Great Question 4 months ago, created a question with more than 5,000 views. For estimation of size factors in DESeq2 analysis
Popular Question 8 months ago, created a question with more than 1,000 views. For HOWTO extract regions from GRanges object
Popular Question 8 months ago, created a question with more than 1,000 views. For HOWTO extract regions from GRanges object
Great Question 9 months ago, created a question with more than 5,000 views. For estimation of size factors in DESeq2 analysis
Popular Question 11 months ago, created a question with more than 1,000 views. For HOWTO extract regions from GRanges object
Popular Question 11 months ago, created a question with more than 1,000 views. For fastqc Exception in thread "Thread-1" (error)
Popular Question 11 months ago, created a question with more than 1,000 views. For HOWTO extract regions from GRanges object
Popular Question 12 months ago, created a question with more than 1,000 views. For HOWTO extract regions from GRanges object
Great Question 12 months ago, created a question with more than 5,000 views. For estimation of size factors in DESeq2 analysis
Popular Question 12 months ago, created a question with more than 1,000 views. For HOWTO extract regions from GRanges object
Popular Question 14 months ago, created a question with more than 1,000 views. For HOWTO extract regions from GRanges object
Great Question 14 months ago, created a question with more than 5,000 views. For estimation of size factors in DESeq2 analysis
Popular Question 15 months ago, created a question with more than 1,000 views. For HOWTO extract regions from GRanges object
Great Question 15 months ago, created a question with more than 5,000 views. For Conditional Coloring Of Heatmaps
Scholar 15 months ago, created an answer that has been accepted. For A: Approximate matching to find similar DNA sequence
Popular Question 16 months ago, created a question with more than 1,000 views. For HOWTO extract regions from GRanges object
Popular Question 17 months ago, created a question with more than 1,000 views. For HOWTO extract regions from GRanges object
Student 19 months ago, asked a question with at least 3 up-votes. For estimation of size factors in DESeq2 analysis

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