Script and data for C. elegenas mirobiome time series analysis

Files

src

abundances.R: abundances plots (barplots, time series)
alpha-diversity.R: within-sample diversity analysis
attribution.R: contribution of species to functions
beta-diversity.R: between-sample diversity analysis
diff-abundance.R: differentially abundant species (DESeq2)
diff-functions.R: differentially abundant functions (DESeq2)
heattree.R: heattree showing differentially abundant species
mca.R: mutiple correspondence analysis of metabolic reactions
nst.R: normalized stochasticity ratio (null model)
over-representation-analysis.R: Over-representation analysis of differentially abundant metabolic pathways
phyloseq.R: analysis of microbial census using phyloseq (filtering, agglomeration)
subsystems_boxplot.R: Differentially abundant function summarized in subsystems determined by DESeq2

CE-CeMbio_V1_revised_20220420.xlsx: Meta data experiment
sample.sheet.tsv: Meta data sequencing
ASV_table.tsv: ASV/OTU table with read counts
tax.own.tbl: Taxonomic classification of ASVs
phyloseq_ps2.RDS: phyloseq object used for further analysis
gtdbtk.bac120.user_msa.fasta.gz_aggregated-rooted.treefile: phylogenetic tree file
diff-functions.csv: differentially abundant functions
cembio.ext_20230818_premed.RDS: metabolic models produced by gapseq
NST.RData: normalized stochasticity ratio results (NST_time.RData, NST_source.RData)
colors_taxa.csv: color codes
uast-*.tbl, gutsmash-*.tbl, medium-*.tbl, fermcs-*.tbl, meta_pwy.tbl, interact-tabale_count.tbl, dbcan-*.tbl: predicted functions for each species