Man pages for SIPmg
Statistical Analysis to Identify Isotope Incorporating MAGs
| 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... |
| 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... |
| samples.object | Fractions table in phyloseq format |
| sample.table | phyloseq-styled sample table |
| scale_features_lm | Scale feature coverage values to estimate their absolute... |
| scale_features_rlm | Scale feature coverage values to estimate their absolute... |
| seq_dil | Sequins dilution table |
| sequins | Sequins table |
| taxonomy.object | Taxonomy table in phyloseq format |
| taxonomy_tibble | Taxonomy table |
| tax.table | phyloseq taxa table from GTDB taxonomy input |
