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We were studying how microglia affect neuronal networks using a standard imaging experiment: 3 mice, 3 coverslips per condition, about 20 neurons measured per coverslip. Our question: Does LPS activation significantly increase PNA signal?
While hierarchical experimental designs are near-ubiquitous in neuroscience and biomedical research, researchers often do not take the structure of their datasets into account while performing statistical hypothesis tests. We present Hierarch, a Python package for analyzing nested experimental designs. Using a combination of permutation resampling and bootstrap aggregation, Hierarch can be used to perform hypothesis tests that maintain nominal Type I error rates and generate confidence intervals that maintain the nominal coverage probability without making distributional assumptions about the dataset of interest.