Sam Lipworth's repositories
ecoli_mic_arg
A repository to accompany the paper "Estimating the effect of antimicrobial resistance genes on minimum inhibitory concentration in Escherichia coli"
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
Deepbinner
a signal-level demultiplexer for Oxford Nanopore reads
dragonflye
:dragon: :fly: Assemble bacterial isolate genomes from Nanopore reads
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
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)
panaroo
An updated pipeline for pangenome investigation
PIRATE
A toolbox for pangenome analysis and threshold evaluation.
pyseer
SEER, reimplemented in python 🐍🔮
resistome_variation
Repository to accompany paper
SNP-IT
Whole genome SNP based identification of members of the Mycobacterium tuberculosis complex
tailfindr
An R package for estimating poly(A)-tail lengths in Oxford Nanopore RNA and DNA reads.