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Moderator: Giovanni M Dall'Olio

gravatar for Giovanni M Dall'Olio
Reputation:
26,900
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Location:
London, UK
Website:
http://bioinfoblog.it/
Twitter:
dalloliogm
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Google Scholar Page
Last seen:
3 weeks, 2 days ago
Joined:
11 years ago
Email:
d*********@gmail.com

Research Associate at the King's College of London. Interested in human population genetics and cancer.

Posts by Giovanni M Dall'Olio

<prev • 1,379 results • page 1 of 138 • next >
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Answer: A: using distinct versions of SEURAT on a SLURM cluster
... Consider using packrat for managing your environment: https://rstudio.github.io/packrat/ ...
written 10 months ago by Giovanni M Dall'Olio ♦ 27k
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Comment: C: How to download fastq from a browser 1000 genomes human chromosome?
... Are you sure you are looking at the correct folder in 1000G? sounds like you are looking at some example folder. ...
written 16 months ago by Giovanni M Dall'Olio ♦ 27k
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Comment: C: How Do I Convert From Bed Format To Gff Format?
... HDF-5 is a generic format for big datasets, which can be used for several applications, from astrophysics to scRNA data. It's conceptually similar to a zip file containing several files and folders. As such, there is not a single way to convert it to plink - it depends on which data is inside the HD ...
written 22 months ago by Giovanni M Dall'Olio ♦ 27k
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Comment: C: Why use LASSO / elastic net in survival regression?
... What about doing a PCA first, then cox or other regressions on the components? The PCA would deal with correlation among the variables. The lasso regression would penalize correlated variables and possibly remove them from the model (as they will have lower betas), but is that what you really want? ...
written 2.2 years ago by Giovanni M Dall'Olio ♦ 27k
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Answer: A: PCA in a RNA seq analysis
... (the following is a dramatization of the reality - but is generally true. You can think of it as the legend of the PCA) For many centuries, the scientific community believed in what is written in the bible, which is that **all humans are created equals, and there are no differences between people** ...
written 2.2 years ago by Giovanni M Dall'Olio ♦ 27k
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Comment: C: PCA in a RNA seq analysis
... If you look at the pairs plots, you will notice that there it seems to be no correlation between any of the components. That in fact is an important property of the components - there is no correlation between them. If you have a dataset containing multiple variables and some of these are correlated ...
written 2.2 years ago by Giovanni M Dall'Olio ♦ 27k
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Comment: C: How to interpret XPEHH (recent selection) score?
... Yes, it is directional but in many cases you don't really know which is the ancestral allele or not. In that case it is safer to get the absolute score, and determine whether there is selection between the two populations, without knowing which is the allele selected. Moreover people tend to calcula ...
written 2.4 years ago by Giovanni M Dall'Olio ♦ 27k
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Answer: A: GTEx Analysis V7 RNA-seq dataset download
... I had trouble downloading the data in the past, luckily the help desk is always very useful and they will answer in a few hours. In the end we managed to find another way to download the data using the cloud. ...
written 3.0 years ago by Giovanni M Dall'Olio ♦ 27k
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Answer: C: as.integer function is converting row names in to number
... Explanation: your column is stored as factors Solution1: as.integer(as.character(mycolumn)) Solution2: use stringAsFactors=F when reading the data ...
written 3.0 years ago by Giovanni M Dall'Olio ♦ 27k
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Comment: C: Boxplot in ggplot2
... This is good but I would use gather from tidyr. The package tidyr is the evolution of reshape2, and it contains more functions to massage data and reshape it for ggplot2/tidyverse. ...
written 3.2 years ago by Giovanni M Dall'Olio ♦ 27k

Latest awards to Giovanni M Dall'Olio

Appreciated 9 weeks ago, created a post with more than 5 votes. For A: Would There Be Interest In A 'Next-Gen Sequencing' Stackexchange Site?
Good Answer 10 weeks ago, created an answer that was upvoted at least 5 times. For A: Would There Be Interest In A 'Next-Gen Sequencing' Stackexchange Site?
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Teacher 4 months ago, created an answer with at least 3 up-votes. For A: What Is The Input Format For Rnaplot In The Vienna Package?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: What Is The Input Format For Rnaplot In The Vienna Package?
Appreciated 6 months ago, created a post with more than 5 votes. For A: Would There Be Interest In A 'Next-Gen Sequencing' Stackexchange Site?
Commentator 8 months ago, created a comment with at least 3 up-votes. For C: Should We Accept The Terms For The Migration To Stackexchange 2.0
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: Should We Accept The Terms For The Migration To Stackexchange 2.0
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Appreciated 19 months ago, created a post with more than 5 votes. For A: Would There Be Interest In A 'Next-Gen Sequencing' Stackexchange Site?
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