Explore @oxfordmmm Open Source projects

Oxford MMM (@oxfordmmm)

oxfordmmm

Stars
38
Global Org. Rank 89,909 (Top 29 %)
Registered about 6 years ago
Most used languages

Python
50.0 %

Nextflow 22.2 %

Rust
5.6 %

Perl
5.6 %

Shell
5.6 %

C++
5.6 %

Jupyter Notebook
5.6 %
Location 🇬🇧 United Kingdom
Country Total Rank 18,196
Country Ranking

Nextflow 27

Perl
560

Rust
1,447

Python
3,950

Jupyter Notebook
4,408

C++
5,844

Shell
6,230

CompassCompact

A compact version of Oxford Compass (Complete Pathogen Analysis Software Solution)

gnomonicus

Python code to integrate results of tb-pipeline and provide an antibiogram, mutations and variants

gumpy

Genetics with numpy

tuberculosis_amr_catalogues

piezo

SARS-CoV2_workflows

grumpy

Re-implementation of gumpy in rust for speed

GenomicDiversityPaper

Scripts for "Genomic diversity affects the accuracy of bacterial SNP calling pipelines"

testdata-catalog

Reposity to keep the catalog of samples for testing

FN5

SNP matrix generation with caching to disk to allow fast reloading

catsup

pre-processing and upload module for SP3

AMR-catalogue-demo

A Jupyter notebook to demonstrate usage of piezo, gumpy and gnomonicus with different AMR catalogues

Jupyter Notebook

speciation

Scripts for Mycobacterium Speciation

catsgo

Command client of SP3 for fetch, run and download.

fn5_pipeline

Nextflow wrapper for FN5

tb-predict-pipeline

Nextflow pipeline for producing variants, mutations and effects of a specified (minos) VCF file

flye_medaka_workflow

Bugflow_DSL2