mjenior Goto Github PK

analysis-scripts

Frequently used bioinformatic scripts I generate

asf_genome_binning

asf_genomic_binning

baxter_fits_microbiome_2016

bigsmall

BacterIal Genome-Scale Metabolic models for AppLied reverse ecoLogy

binning

Scripts required to calculate tetramer frequencies and create input files for ESOM. See: Dick, G.J., A. Andersson, B.J. Baker, S.S. Simmons, B.C. Thomas, A.P. Yelton, and J.F. Banfield (2009). Community-wide analysis of microbial genome sequence signatures. Genome Biology, 10: R85

blog_scripts

A repo to house the scripts I create and write about in my thesis project blog (http://mjenior.github.io/)

cn_proxy

Content Negotiation Proxy for CrossRef DOIs

cobrapy

COBRApy is a package for constraint-based modeling of biological networks

demo_repo

Demonstrating how GitHub and GitKraken work!

hacker-scripts

Based on a true story

klebsiella_2021

megahit

MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

mjenior.github.io

Personal Research Website

ml_for_hackers

Code accompanying the book "Machine Learning for Hackers"

modeling_tools

pschloss

Pat Schloss's repository

reconstructor

Automated GENRE building from gene fastas

riptide

Reaction Inclusion by Parsimony and Transcript Distribution

schlosslab.github.io

The website for the Schloss Lab at the University of Michigan

scripts

General scripts used in the lab. Almost all of them are in core perl, i.e require no modules that don't already come with a perl installation. These script are currently in use by the Lab, so expect full support. This material is based upon work supported by the National Science Foundation under Grant Number EAR-1035955. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

smith_etal_enterococcus

C. difficile metabolic modeling in co-culture with E. faecalis

styles

Official repository for Citation Style Language (CSL) citation styles.

water-use

Visualization using USGS water use data.