DESeq2_l2fc             Calculating log2 fold change for HTS-SIP data.
GC_content              GC_content table
HRSIP                   (MW-)HR-SIP analysis
as.Num                  The following function is adapted from HTSSIP R
                        package conversion to numeric
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
phyloseq2df             The following function is adapted from HTSSIP R
                        package phyloseq data object conversion to
                        data.frame
phyloseq2table          The following function is adapted from HTSSIP R
                        package Phyloseq conversion to a
                        ggplot-formatted table
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
