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benw

This is a test repo for software carpentry lesson.

chipseqconsolidationprocessing

ChIP-seq processing code used in Minch et al. 2014

chipseqprocessing

cobratoolbox

COnstraints Based Reconstruction and Analysis toolbox for MATLAB

compass

In-Silico Modeling of Metabolic Heterogeneity using Single-Cell Transcriptomes

democracyandroidapp

jenior_riptide_2020

Repository associated with RIPTiDe publication

mcadre

metabolic Context-specificity Assessed by Deterministic Reaction Evaluation (mCADRE) for generating draft tissue-specific metabolic models

mtb_matlab_py

MATLAB and Python code for MTB stuff

mtbmiscshellscripts

Miscellaneous Shell Scripts from CIDR

mtbprom2.0

Code and files for performing transcription factor knockout and overexpression simulations on genome-scale regulatory-metabolic models using the updated PROM framework.

mtbregmetanal

code for PROM and associated regulatory-metabolic network analysis

pabio536

A collection of files for the University of Washington class Pathobiology 536

pabio536-basicplotting

Jupyter Notebook about Basic Plotting for PABIO536

ratcon1

Reconciled rat and human metabolic networks for comparative toxicogenomics analyses and biomarker predictions

scpythonday3

shuyim-sofwarecarpentry

This is a test repo for software carpentry lesson.

spoon-knife

This repo is for demonstration purposes only. Comments and issues may or may not be responded to.

starcluster_scripts

scripts used in analyses on starcluster