Friday, 6 May 2016

Assessing read depth variation based on a bam file

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I have a BAM file of sequencing reads mapped to an assembly (that was made based on those sequencing reads), and would like to know whether ...
Friday, 15 April 2016

Clustering and heatmaps in R

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I wanted to read in a data file of distances, and carry out some clustering in R. For my data, I have a set of species in which I have dru...
Friday, 18 March 2016

Getting orthologs and their percent identity from WormBase ParaSite

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There are two assemblies for Fasciola hepatica in WormBase ParaSite , for two different isolates. I wanted to get the orthologs for them, an...
Friday, 19 February 2016

Extract phenotypes/GO terms for C. elegans genes from WormBase

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I had a list of C. elegans genes (WBGene identifiers) and wanted to know which C. elegans genes have known phenotypes. On the WormBase page,...
Thursday, 18 February 2016

Calculating distances between drug molecules

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Cluster a set of compounds by structural similarity Given a set of drug molecules from Chembl , I need to calculate pairwise distances bet...
Thursday, 7 January 2016

Search across multiple pdfs at once

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To search across multiple pdfs at once for a phrase (eg. 'fatty acid'): - open one file in Acrobat reader - press Mac-key(Command ...
Thursday, 17 December 2015

Orthofinder for orthologs

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Today I heard of a new software for finding orthologs and paralogs, called Orthofinder (published by Emms and Kelly 2015), which my former ...