This repository includes the code used in our multiomics BMI study.

University of Cambridge PhD thesis

Code to reproduce the analysis of "Decoding gene regulation in the mouse embryo using single-cell multi-omics""

MOFA training resources

Repository for the ISMB/ECCB workshop "A practical introduction to multi-omics integration and network analysis"

all my dirty r-scripts

Detecting and treating outliers in Python

Miscellaneous scripts

Quickly calculate coverage of sequences in a .sam file while retaining breadth information

Scripts in support of publication

Collection of (mostly bioinformatics) scripts that I use in day-to-day work

Scripts

Ultra-deep search for novel viruses

Long-reads Gap-free Chromosome-scale Assembler

Just a Microbiology System (JAMS) - a suite for analyzing microbiological sequencing data for use on NIH HPC systems (Biowulf)

Welcome to the mothur project, initiated by Dr. Patrick Schloss and his software development team in the Department of Microbiology & Immunology at The University of Michigan. This project seeks to…

A fast and sensitive gapped read aligner

Jupyter notebooks and data from Ruaud and Esquivel-Elizondo

The SQL database schema files for the antiSMASH DB

Scripts to generate the databases for antiSMASH's ClusterBlast and KnownClusterBlast.

Uniform Manifold Approximation and Projection

basic tools for computing alignment-free sequence comparison measures

MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data

HUMAnN is the next generation of HUMAnN 1.0 (HMP Unified Metabolic Analysis Network).

MaAsLin2: Microbiome Multivariate Association with Linear Models

useful scripts to process DNA info