User: Konstantinos Yeles

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110
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Trusted
Location:
Italy
Last seen:
1 month, 1 week ago
Joined:
1 year, 10 months ago
Email:
y*****************@gmail.com

Posts by Konstantinos Yeles

<prev • 26 results • page 1 of 3 • next >
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Comment: C: Parallelization in R 2020
... In some cases that I have more than 10,000 GRs per Chr, I split them into chunks, and instead of using chromosomes, I use these chunks to perform the parallelized downstream functions. ...
written 11 weeks ago by Konstantinos Yeles110
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Comment: C: Parallelization in R 2020
... @ATpoint Most of the time I work on Bioconductor Docker containers, otherwise Windows laptop. In my project, I work with Genomic ranges so an approach "per chromosome" should be more suitable I think. I use also packages such as bumphunter, derfinder etc. @Jean-Karim Heriche Should I move it to Sta ...
written 11 weeks ago by Konstantinos Yeles110
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Parallelization in R 2020
... Hello Biostars, I would like to ask about the latest "news" about parallelization in R. I have searched a bit through various articles/posts on Biostars and StackOverflow but most of them are quite old. Has someone tried to benchmark the latest parallelization packages in R checking on versatili ...
R parallel doparallel biocparallel snowfall written 11 weeks ago by Konstantinos Yeles110 • updated 11 weeks ago by zx87549.4k
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Answer: A: Best way to find novel non-coding transcripts from stranded RNA-seq data
... Maybe you could use the workflow of [derfinder package][1] If you are familiar with [recount2][2] and RailRNA[enter link description here][3] aligner is an annotation agnostic workflow that probably could be utilised to find novel transcripts. [1]: https://www.bioconductor.org/packages/rele ...
written 8 months ago by Konstantinos Yeles110
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Comment: C: publicly available data
... @ATpoint Well someone bought it in the first place :) ...
written 10 months ago by Konstantinos Yeles110
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Comment: C: publicly available data
... @genomax What would have been the practical considerations regarding direct access to the data? (In the first place of course, now it's late, as you have already said that it would need a lot of work computationally and time/manpower consuming) Is there any data with respect to how many studies com ...
written 10 months ago by Konstantinos Yeles110
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Comment: C: publicly available data
... @ATpoint But wouldn't be possible to be improved in the future? @genomax I understand that it's not a trivial task, but why it wasn't included from the start. Since the time that GEO and ArrayExpress became available why they haven't linked them directly? ...
written 10 months ago by Konstantinos Yeles110
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Comment: C: publicly available data
... > Some journals such as Cell now even have the accession number on the publically-available front page (abstract page) of the paper. Exactly, that's what I expect also to be the case for every entry in a Pubmed publication. As every entry has the abstract then it can have also a link to the data ...
written 10 months ago by Konstantinos Yeles110
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Forum: publicly available data
... Dear Biostars, Most of the students/researchers use PubMed in order to find publications relative to their work or the field of interest. Although Pubmed, most of the time, includes the links of the journal that each publication is published it doesn't have the **data**. Why a link directly to GEO ...
geo sra forum arrayexpress written 10 months ago by Konstantinos Yeles110 • updated 9 months ago by h.mon30k
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Answer: A: DESeq2 (or EdgeR) Exploratory Analysis with no Replicates
... In addition to the EdgeR manual, you could use the [NOISeq][1] package that has a function precisely for cases without biological replication. manual: https://bioconductor.org/packages/release/bioc/vignettes/NOISeq/inst/doc/NOISeq.pdf chapter 5.1.2 NOISeq-sim: no replicates available Good luck wi ...
written 10 months ago by Konstantinos Yeles110

Latest awards to Konstantinos Yeles

Popular Question 4 months ago, created a question with more than 1,000 views. For smallRNA sequencing workflow and Database usage
Supporter 20 months ago, voted at least 25 times.
Student 21 months ago, asked a question with at least 3 up-votes. For smallRNA sequencing workflow and Database usage

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