samlipworth Goto Github PK

bactdating

Bayesian inference of ancestral dates on bacterial phylogenetic trees

base_changer

Changes bases in a fasta file at user specified positions

binder

Adds binder to tidyverse, providing JupyterHub

coder

Classification of Cases into Deterministic Categories

coronavirus-dashboard-api-r-sdk

Coronavirus (COVID-19) in the UK - API Service SDK for R

covid_amr

dcsi

Diabetes complication severity index

deepbinner

a signal-level demultiplexer for Oxford Nanopore reads

dragonflye

:dragon: :fly: Assemble bacterial isolate genomes from Nanopore reads

ecoli_mic_arg

A repository to accompany the paper "Estimating the effect of antimicrobial resistance genes on minimum inhibitory concentration in Escherichia coli"

finalfit

Quickly create elegant regression results tables and plots when modelling in R

flanker-1

Gene-flank analysis tool

flanker-reproducible-example

Binder repo for making figures in Matlock/Lipworth et al (Flanker Paper)

gratia_sam

ggplot-based graphics and useful functions for GAMs fitted using the mgcv package

heaps

hybrid_pipeline

influenza

kvarq-mtbc-snp-barcodes

Mycobacterium tuberculosis complex SNP barcoding, after Coll 2014

lrh2h

mab_ariba

ariba library for predicting clarithromycin resistance in M. abscessus

nf_tutorial

learning to use nf

ont-wash-hybrid

Code used for analysis in the paper Optimised use of Oxford Nanopore Flowcells for Hybrid Assemblies (Lipworth et al 2020)

oxford_ecoli_kleb

panaroo

An updated pipeline for pangenome investigation

pirate

A toolbox for pangenome analysis and threshold evaluation.

planets

pyseer

SEER, reimplemented in python 🐍🔮

resistome_variation

Repository to accompany paper

rna_methods

short_read_h2h