DESeq2_l2fc             Calculating log2 fold change for HTS-SIP data.
GC_content              GC_content table
HRSIP                   (MW-)HR-SIP analysis
atomX                   Atom fraction excess table
calc_Mheavymax_MAGs     Calculate Mheavymax
calc_atom_excess_MAGs   Calculate atom fraction excess
coverage_normalization
                        Normalize feature coverages to estimate
                        absolute abundance or relative coverage using
                        MAG/contig coverage values with or without
                        multiplying total DNA concentration of the
                        fraction
df_atomX_boot           Bootstrapped atom fraction excess table
f_tibble                Coverage table
filter_l2fc             Filter l2fc table
filter_na               Remove MAGs with NAs from atomX table
fractions               Fractions table
incorporators_taxonomy
                        Isotope incorporator list with GTDB taxonomy
mag.table               MAG abundance table in phyloseq format
phylo.qSIP              Master phyloseq object
phylo.table             Master phyloseq object using the MAG phyloseq
                        objects
qSIP_atom_excess_MAGs   Calculate atom fraction excess using q-SIP
                        method
qSIP_atom_excess_format_MAGs
                        Reformat a phyloseq object of
                        qSIP_atom_excess_MAGs analysis
qSIP_bootstrap_fcr      Calculate adjusted bootstrap CI after for
                        multiple testing for atom fraction excess using
                        q-SIP method. Multiple hypothesis tests are
                        corrected by
sample.table            phyloseq-styled sample table
samples.object          Fractions table in phyloseq format
scale_features_lm       Scale feature coverage values to estimate their
                        absolute abundance
scale_features_rlm      Scale feature coverage values to estimate their
                        absolute abundance
seq_dil                 Sequins dilution table
sequins                 Sequins table
tax.table               phyloseq taxa table from GTDB taxonomy input
taxonomy.object         Taxonomy table in phyloseq format
taxonomy_tibble         Taxonomy table
