User: Konstantinos Yeles

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Italy/Salerno
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Posts by Konstantinos Yeles

<prev • 22 results • page 1 of 3 • next >
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Comment: C: publicly available data
... @ATpoint Well someone bought it in the first place :) ...
written 7 days ago by Konstantinos Yeles50
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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 7 days ago by Konstantinos Yeles50
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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 8 days ago by Konstantinos Yeles50
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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 8 days ago by Konstantinos Yeles50
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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 8 days ago by Konstantinos Yeles50 • updated 5 days ago by h.mon27k
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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 4 weeks ago by Konstantinos Yeles50
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Answer: A: RIP-Seq data analysis
... You can use [RIPSeeker][1] package from Bioconductor, or you could perform a "differential enrichment" analysis with [edgeR][2] / [DESeq2][3] packages. [1]: https://www.bioconductor.org/packages/release/bioc/html/RIPSeeker.html [2]: https://www.bioconductor.org/packages/release/bioc/html/edge ...
written 10 weeks ago by Konstantinos Yeles50
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Comment: C: How to transform my TCGA data into this?
... You could use tidyverse to do these manipulations, I suggest you to read this: https://r4ds.had.co.nz/introduction.html In the 5th chapter, you will find easy ways to do it. As @ATpoint mentioned, you will need these skills if you are going to work as a bioinformatician/data analyst. Tips : spread/g ...
written 10 weeks ago by Konstantinos Yeles50
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Comment: C: RIP-seq identifing reverse complement reads between smallRNA and targeted mRNA
... Then I could use R to subset the BED and then use it with bed tools Thanks. Is it possible to post it as an answer? ...
written 6 months ago by Konstantinos Yeles50
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Comment: C: RIP-seq identifing reverse complement reads between smallRNA and targeted mRNA
... I have reads from a BAM file of length <45 and reads 45< rl < 80. I have aligned them and now I'm looking to check if between these sets there is a matching. ...
written 6 months ago by Konstantinos Yeles50

Latest awards to Konstantinos Yeles

Supporter 10 months ago, voted at least 25 times.
Student 11 months ago, asked a question with at least 3 up-votes. For smallRNA sequencing workflow and Database usage

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