avrilomics
tales of adventures and misadventures in bioinformatics
Thursday 16 May 2024
Testing whether data follow a uniform distribution
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Someone asked me how to test whether a data variable, which has values ranging from 1-1000, follows a uniform distribution. Getting some in...
Thursday 2 May 2024
Finding SNPs in a core gene alignment using snp-sites
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Today I'm using the snp-sites software (by Page et al 2016 ) to extract SNPs from core gene alignments (output from Panaroo ). It's...
Tuesday 23 April 2024
'Practical Statistics for Medical Research' by Douglas G. Altman
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I'm doing some Statistics revision, reading the brilliant and classic book ' Practical Statistics for Medical Research ' by Doug...
Friday 12 January 2024
We're hiring - Training and Events Coordinator
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We are currently recruiting in Nick Thomson's group at the Wellcome Sanger Institute for a 'Training and Events Coordinator' t...
Thursday 11 January 2024
Finding core genes shared by a bacterial species using Panaroo
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This week I learnt how to use the Panaroo software for finding core genes (genes present across all isolates of a species) shared across a ...
Friday 5 January 2024
Predicting bacterial genes using Prokka
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I've been predicting genes in bacterial assemblies using Prokka . The Prokka software has been described in this paper by Seemann (2014...
Tuesday 19 December 2023
Visualisation using Cytoscape of a PopPUNK database
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Earlier I wrote about how I made a visualisation of my PopPUNK database using Microreact: see the blogpost here . Today I'm going to tel...
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