Reilly Cooper's repositories
daphnia_magna_metagenome
All scripts used for data analysis and visualization in "Characterization of core bacterial species in the Daphnia magna microbiota using shotgun metagenomics".
ab-targeting-daphnia
Targeted manipulation of abundant and rare taxa in the Daphnia magna microbiota with antibiotics impacts host fitness differentially. Reilly O. Cooper, Janna M. Vavra, Clayton E. Cressler.
anvio
An analysis and visualization platform for 'omics data
bioutils
A collection of Python code that I use more often than not
circadian_microbiome
This project contains code for: Pfenning-Butterworth A.C, Cooper R.O., and Cressler C.E. Diel rhythm influences microbiota composition in two zooplankton species.
daphnia_multigenerational_antibiotics
Multiple generations of antibiotic exposure and isolation influence host fitness and the microbiome in a model zooplankton species. Cooper RO, Tjards S, Hotovy J, Nguyen DT, Cressler CE.
PatientRiskAssessment
A patient risk assessment iOS application as part of the Hack:Now hackathon competition
pyani
Python module for average nucleotide identity analyses