User: Aerval

gravatar for Aerval
Aerval240
Reputation:
240
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Trusted
Location:
Germany
Last seen:
4 days, 12 hours ago
Joined:
3 years, 6 months ago
Email:
r**************@gmail.com

PhD student from Berlin, Germany

Posts by Aerval

<prev • 44 results • page 1 of 5 • next >
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Comment: C: Multisample DMR calling
... Thanks, that looks interesting. I am not working on that particular project anymore but will forward your link to the people still working on it. ...
written 10 days ago by Aerval240
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Job: PhD student position in bioinformatics (sequence analysis, functional genomic, data mining, ML) at BIH, Berlin, Germany
... We are looking for a PhD student in computational biology/bioinformatics who will join Martin Kircher’s Junior Research Group at the Berlin Institute of Health in Germany. Starting date is January 1st, 2018 or later. The group does research in the areas of **sequence analysis, data mining and functi ...
machine learning genomics variant effect mpra job written 10 days ago by Aerval240
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Comment: C: Survey/Vote: If you could double the speed of any three commandline tools, which
... I wondered, would a linear sorting algorithm like radixsort improve that or are indexing and later random accessing the sorted lines the bottle neck. I mean, formats like bed or vcf have nicely defined columns that need to be sorted most of the times. ...
written 15 days ago by Aerval240
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Answer: A: Threshold for Differentially Methylated Regions
... You cannot set a definitive threshold when change in methylation is meaningful. Sure, a single cell is always 1, 0.5 or 0 methylated at one site, but you have bulk data from probably thousands of cells. Statistical tests are for sure the way to go but differ (depending on your type of data and some ...
written 6 months ago by Aerval240
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Answer: A: Bisulfite sequencing query
... You wont get a definite answer here as there is not that BS protocol, there is WGBS, RRBS, 450/850k arrays that are equally important. A good introduction will be Christoph Bocks review: http://www.nature.com/nrg/journal/v13/n10/full/nrg3273.html ...
written 8 months ago by Aerval240
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Comment: C: CpG Island prediction
... I do not have an overview over the field and therefore cannot add much but would suggest not to look at omictools.com. Their list is almost certainly incomplete and outdated like in this case where the three tools labelled "new" (including newcpgreport and cpgplot) are from 1999, 1999 and 1992! That ...
written 8 months ago by Aerval240
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Comment: C: CpG coverage of BS-seq ?
... Sorry if I misused the term dinucleotide, I meant both cytosines in a CpG double strand site. So one CpG. ...
written 8 months ago by Aerval240
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Answer: A: CpG coverage of BS-seq ?
... CpG usually means the CpG dinucleotide (and is afaik specified otherwise if not). When you use bsseqs `getCov` you get the number of + and - strand reads. (I have no idea about RRBS as I am working with WGBS) ...
written 8 months ago by Aerval240
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Comment: C: Looking for a Bioinformatics Internship in Europe
... Hey Nephtali, I think you need to specify your interest more. Bioinformatics is a broad field and there are hundereds of groups in Europe (in academia, you are not specifying whether you want to go there or into industry), you might get a contact through this but honestly I in your position would r ...
written 9 months ago by Aerval240
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Answer: A: Segmentation method comparisons: HMM, CBS, RS
... Well, DSS only looks for consecutive CpGs which reach a certain p-value, though thats also a HMM to some degree. The review I have most of my information from is Robinoson et al. 2014: (Statistical methods for detecting differentially methylated loci and regions). If you have more I would also be i ...
written 10 months ago by Aerval240

Latest awards to Aerval

Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Advice for undergraduate bioinformatics learners
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: Advice for undergraduate bioinformatics learners
Autobiographer 3.1 years ago, has more than 80 characters in the information field of the user's profile.

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