All Posts - John Lees' blog

All Posts

2019

Conservation of core genes in S. pneumoniae 04-17

Using unitigs for bacterial GWAS with pyseer 04-08

Paper summary – PopPUNK for bacterial epidemiology 01-25

2018

Creating a conda package with compilation and dependencies 10-15

conda build: libarchive: cannot open shared object file: No such file or directory 10-09

Linear scaling of covariances 09-14

Expression modules in S. pneumoniae 04-24

2017

Installing phyx without sudo 11-24

setup.py not found using pip install 11-20

Firth regression in python 11-08

Running BSLMM in gemma 08-23

Tanglegrams can be misleading 02-22

2016

Likelihood ratio test in SEER 10-27

Sorting a massive file 10-13

Removing helperamc (Advanced Mac Cleaner) OS X 10-03

Running bugwas + gen files 09-08

Mean coverage from a BAM one-liner 05-25

R packages break after OS X upgrade 03-10

Installing PEER executable peertool 01-19

2015

Simulate disease state from a given odds ratio, fraction exposed, fraction affected 10-09

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