pex_types

R scripts used for S. Widder, L. Carmody, K. Opron, L. Kalikin, L. Caverly, J. LiPuma "Microbial community organization designates distinct pulmonary exacerbation types and predicts treatment outcome in cystic fibrosis."

NAVIGATION

MAIN FIGURES AND ANALYSES

R scripts for respective figures located in directories

FIG1_CLUSTERING

FIG2_TIME_DEPENDENCY

FIG3_NW

FIG4_PATHOGENROLE

AUXILIARIES

DATA_INPUT

Phyloseq object storing data & metadata is labeled "EC880F1B.rda"

DATA_INPUT/NWs

Time series-wise collection of inferred co-occurrence graphs & topology parameters

HARMONIZE_FIGURES

Auxiliary functions for main and supplemental figures, will be sourced automatically

SUPPLEMENTAL FIGURES AND ANALYSES

R scripts for supplemental figures located in directories

SUPP_FIG1

SUPP_FIG2

Input data hosted at Zenodo with doi 10.5281/zenodo.11109986

SUPP_FIG3

Generative code in FIG2_TIME_DEPENDENCY, FIG1_CLUSTERING/1BCD_PCA_CLUSTERING_CHI

SUPP_FIG4

SUPP_FIG5

Generative code in FIG2_TIME_DEPENDENCY

SUPP_FIG6

SUPP_FIG7