User: Assa Yeroslaviz

gravatar for Assa Yeroslaviz
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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1 day, 8 hours ago
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6 years, 2 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 • 286 results • page 1 of 29 • next >
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genome-wide gene occupancy profiles
... Hi, I was wondering if there is a tool for plotting gene expression profiles over multiple genes. We have analyzed a chipseq experiment with multiple samples of different time points. For each time point we expect the transcription to behave differently due to our knockout. We would like to plot t ...
bedgraph chip-seq occupany profile written 17 days ago by Assa Yeroslaviz1.1k
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ChIP-chip ANalysis of NimbleGen tiling arrays
... Hi, I have an older data set of NimbelGen tiling arrays I need to analyze. I am looking for tools/package to do some peak calling (identifing enriched region on different samples) as well as Differential binding analysis (comparing enriched regions between samples / conditions). I would appreciate ...
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how to calculate with metadata of GRanges Objects
... From a ChIPseq experiment we're having I'm reading the bigwig files as `GRanges` objects into R. One file for the IP sample, one for the Input. The peak values are saved as the score of the Granges object. As we have two different control samples (input and IgG), I would like to calculate the score ...
rtracklayer macs2 bigwig granges genomicranges written 4 weeks ago by Assa Yeroslaviz1.1k
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Comment: C: How does differences in library size infuences ChIP-Seq experiments?
... Thanks, I know the normalisation is different and dependent from one method to the other. My worries are mainly due to the huge differences between the library sizes. Independent of the algorithm, is it possible to handle such a big difference between the libraries? ...
written 3 months ago by Assa Yeroslaviz1.1k
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How does differences in library size infuences ChIP-Seq experiments?
... I have a ChIP-Seq experiment, with two knock-outs and one WT from three different time-points. For each of them I have IP and input samples in duplicates. In addition I have IgG samples (also in duplicates) for each of the conditions (only for time-point 0). My problem is that the library sizes va ...
chip-seq library normalisation written 3 months ago by Assa Yeroslaviz1.1k • updated 3 months ago by Istvan Albert ♦♦ 73k
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Comment: C: Read a text file into a list
... me neither, I will try it though ...
written 5 months ago by Assa Yeroslaviz1.1k
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Comment: C: Read a text file into a list
... yes i know. I wish I could. I can't change the input files. This is how I got them. I think this is a list structure exported to a text file. ...
written 5 months ago by Assa Yeroslaviz1.1k
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Comment: C: Read a text file into a list
... this look very nice (and tidy :D ). thanks ...
written 5 months ago by Assa Yeroslaviz1.1k
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Comment: C: Read a text file into a list
... thanks for the links. I have seen them all before I posted this question here. I have tried them, but couldn't get what I was trying to do. I know there are supposedly plenty of ways to achieve it. I just can't do it myself. IMHO this is still bioinformatics related, as it related to R, it works o ...
written 5 months ago by Assa Yeroslaviz1.1k
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Comment: C: Read a text file into a list
... thanks for the advice, but as I mentioned above, this is not what i want to achieve. I would like to keep each group as one vector in a list of vectors. ...
written 5 months ago by Assa Yeroslaviz1.1k

Latest awards to Assa Yeroslaviz

Popular Question 4 days ago, created a question with more than 1,000 views. For HOWTO extract regions from GRanges object
Popular Question 16 days ago, created a question with more than 1,000 views. For HOWTO extract regions from GRanges object
Great Question 20 days ago, created a question with more than 5,000 views. For Go Enrichment Of Rna-Seq Data
Popular Question 7 weeks ago, created a question with more than 1,000 views. For HOWTO extract regions from GRanges object
Popular Question 9 weeks ago, created a question with more than 1,000 views. For HOWTO extract regions from GRanges object
Prophet 12 weeks ago, created a post with more than 20 followers. For The Difference Between Directional And Nondirectional Sequencing
Good Question 12 weeks ago, asked a question that was upvoted at least 5 times. For following Kallisto with DESeq2 using tximport package
Popular Question 5 months ago, created a question with more than 1,000 views. For fastqc Exception in thread "Thread-1" (error)
Popular Question 5 months ago, created a question with more than 1,000 views. For Expression Profiles Of Proteins
Popular Question 5 months ago, created a question with more than 1,000 views. For HOWTO extract regions from GRanges object
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Popular Question 5 months ago, created a question with more than 1,000 views. For CLC GW vs. tophat2
Student 5 months ago, asked a question with at least 3 up-votes. For Expression Profiles Of Proteins
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Great Question 6 months ago, created a question with more than 5,000 views. For Heat Map With Two Color Scales
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Popular Question 8 months ago, created a question with more than 1,000 views. For Raw Data From Solid Sequencing
Popular Question 8 months ago, created a question with more than 1,000 views. For Raw Data From Solid Sequencing

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