User: Agapow

gravatar for Agapow
Agapow270
Reputation:
270
Status:
Trusted
Location:
London, UK
Website:
http://www.agapow.net
Last seen:
6 years, 5 months ago
Joined:
8 years, 1 month ago
Email:
p**@agapow.net

Computational biologist, specialising in infectious disease, evolution and phylogenetics. On the job market - drop me a line.

Posts by Agapow

<prev • 7 results • page 1 of 1 • next >
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Answer: A: Measure For The Separation Of Phenotypic Groups On An Unrooted Phylogenetic Tree
... In the past when I've had to do such a thing, I've measured a clustering or imbalance metric across the phenotypes in question and then compared that to trees in which the states were repeatedly randomized. Thus you get some sort of confidence for the separation of the two states against a case wher ...
written 6.5 years ago by Agapow270
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Answer: A: Preferred Tools For Making Analysis Pipeline Flowchart ?
... There's no single good tool for this sort of this as you may have gathered. All you can ask for is a good flowcharting tool. I'm partial to yEd (http://www.yworks.com/en/productsyedabout.html), which seems to strike a balance between power and ease of use. ...
written 6.5 years ago by Agapow270
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Comment: C: Associating Viral Sequence With Epidemiological Data
... Individual case data, dates, outcomes, the whole paella. ...
written 8.0 years ago by Agapow270
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Comment: C: A Pwm With Gapped Alignments In Biopython
... Which lead me to finally writing down all my notes on Alphabets: http://www.agapow.net/science/bioinformatics/alphabets-in-biopython ...
written 8.0 years ago by Agapow270
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Answer: A: A Pwm With Gapped Alignments In Biopython
... Just quickly: the proximate problem here is that the alphabets of the Motif and and aligned sequence being added have to be the same (see line 44 of _Motif.py). So you could create the motif with the same alphabet, or perhaps try to set it to None, which with avoid the alphabet comparison. Biopython ...
written 8.0 years ago by Agapow270
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Associating Viral Sequence With Epidemiological Data
... The setup: I have a large number of sequences from a viral pathogen and the associated epidemiological data, collected during a major disease outbreak. I deeply suspect that the varied epidemiology seen across the outbreak (case severity and outcomes, transmission rate, etc.) is the result of change ...
evolution association snp written 8.0 years ago by Agapow270 • updated 8.0 years ago by David Quigley11k
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Answer: A: Best Language For Introductory Programming Course From Within An Introduction Co
... There was a lengthy discussion on this at LinkedIn, and I'm going to largely repeat my comments from there. You'll get a lot of different opinion on this because: it's a religious issue (i.e. comes down a lot to subjective judgements and personal experience), and there's a lot of possible consider ...
written 8.1 years ago by Agapow270

Latest awards to Agapow

Autobiographer 6.5 years ago, has more than 80 characters in the information field of the user's profile.
Student 8.0 years ago, asked a question with at least 3 up-votes. For Associating Viral Sequence With Epidemiological Data
Good Answer 8.1 years ago, created an answer that was upvoted at least 5 times. For A: Best Language For Introductory Programming Course From Within An Introduction Co
Teacher 8.1 years ago, created an answer with at least 3 up-votes. For A: Best Language For Introductory Programming Course From Within An Introduction Co

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