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an-introduction-to-applied-bioinformatics

Interactive lessons in bioinformatics.

computational_biology

Example GitHub repository for Computational Biology

coral_disease_datasets

Standardized Coral Disease Datasets for Metaanalysis

demographics

scripts associated with analysis of student demographic data for UW Bothell

full_spectrum_bioinformatics

An open-access bioinformatics text

gcmp_analysis_2024

latest analysis for GCMP data including Neutral Model Analysis

gcmp_australia_coevolution

Code and intermediate data files for the Global Coral Microbiome Project's Study of coral-microbe cophylogeny in Australia

gcmp_genomics

A repository for comparing coral innate immune gene profiles to Global Coral Microbiome Project datasets.

gcmp_global_disease

This project hold the workflow for the Global Coral Microbiome Project's global comparison of coral disease susceptibility and microbiome structure.

genome_skimming

Benchmarks and analysis code for skimming of coral genomes

intro_to_data_studies

karenina

Simulation and modeling tools for studying Anna Karenina effects in animal microbiomes

lab_safety

Laboratory with Lab Safety Information, Templates, and Issues

md_menagerie

The Metadata Menagerie is a collection of tools for manipulation and graphing of metadata files for microbial ecology research. Current status is simply a collection of scripts developed for other projects (not intended for external consumption). This description will be updated when the collection is ready for external use.

mws

organelle_removal

picrust

Phylogenetic Investigation of Communities by Reconstruction of Unobserved STates (PICRUST): Official repository for software and unit tests

q2-karenina

QIIME2 plugin for the karenina package for modeling stochastic microbiome dynamics

qcli

Tools for developing and testing command line interfaces in Python.

resilient_vs_susceptible_mcapitata

Microbiome analysis pipeline files for the resilient vs suscepible Montipora capitata proteomics study.

rorschach

smeagl

SMEAGL (Simulated Microbial Evolution and Genomic LGT) is designed to simulate microbial ecology and evolution. The initial application is to explore the hypothesis that high abundances of DNA mobility elements in some deep sea hydrothermal vent microbiomes may be more strongly selected in low-richness communities

uwb_hyak_resources

Resources for users of the UWB Hyak nodes

viroscape

Tools for analysis of viral consortia with DNA sequencing