atomX |
Atom fraction excess table |
calc_atom_excess_MAGs |
Calculate atom fraction excess |
calc_Mheavymax_MAGs |
Calculate Mheavymax |
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 |
DESeq2_l2fc |
Calculating log2 fold change for HTS-SIP data. |
df_atomX_boot |
Bootstrapped atom fraction excess table |
filter_l2fc |
Filter l2fc table |
filter_na |
Remove MAGs with NAs from atomX table |
fractions |
Fractions table |
f_tibble |
Coverage table |
GC_content |
GC_content table |
HRSIP |
(MW-)HR-SIP analysis |
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_format_MAGs |
Reformat a phyloseq object of qSIP_atom_excess_MAGs analysis |
qSIP_atom_excess_MAGs |
Calculate atom fraction excess using q-SIP method |
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 |
sequins |
Sequins table |
seq_dil |
Sequins dilution table |
tax.table |
phyloseq taxa table from GTDB taxonomy input |
taxonomy.object |
Taxonomy table in phyloseq format |
taxonomy_tibble |
Taxonomy table |