Code and data from "Quantifying the Adaptive Potential of a Nascent Bacterial Community"
Each experiment ("E") folder has the following files/subdirectories:
E_x_exps.csv - list of experiments/replicates
E_x_meta.csv - metadata for each experiment
cfus/ - time-resolved colony counts
data/bc_counts/ - final barcode read counts, merged with genomic barcode locations
data/errorcorrectedcodes/ - barcode counts after second error correction
data/errorcorrectedcodes0/ - barcode counts after first error correction
data/fitness/ - inferred fitness values for each gene
data/kt_errors/ - estimated variance parameters
data/meanfitness/ - estimated mean fitness dynamics
data/MultiCode_tables/ - output of MultiCode.pl
data/outliers/ - lists of putative outliers