Statistical Analysis to Identify Isotope Incorporating Metagenomic Features
The following function is adapted from HTSSIP R package conversion to ...
Calculate atom fraction excess
Calculate Mheavymax
Normalize feature coverages to estimate absolute abundance or relative...
Calculating log2 fold change for HTS-SIP data.
Filter l2fc table
Remove MAGs with NAs from atomX table
(MW-)HR-SIP analysis
Isotope incorporator list with GTDB taxonomy
Master phyloseq object using the MAG phyloseq objects
The following function is adapted from HTSSIP R package phyloseq data ...
The following function is adapted from HTSSIP R package Phyloseq conve...
Reformat a phyloseq object of qSIP_atom_excess_MAGs analysis
Calculate atom fraction excess using q-SIP method
Calculate adjusted bootstrap CI after for multiple testing for atom fr...
phyloseq-styled sample table
Scale feature coverage values to estimate their absolute abundance
Scale feature coverage values to estimate their absolute abundance
phyloseq taxa table from GTDB taxonomy input
Statistical analysis as part of a quantitative stable isotope probing (SIP) metagenomics study to identify isotope incorporating metagenomic features. Helpful reading and a vignette in bookdown format is provided on the package site <https://zielslab.github.io/SIPmg.github.io/>.