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SIPmg (version 3.0)

Statistical Analysis to Identify Isotope Incorporating Metagenomic Features

Description

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 .

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Version

Install

install.packages('SIPmg')

Monthly Downloads

44

Version

3.0

License

GPL-2

Maintainer

Pranav Sampara

Last Published

September 24th, 2025

Functions in SIPmg (3.0)

taxonomy_tibble

Taxonomy table
scale_features_rlm

Scale feature coverage values to estimate their absolute abundance
scale_features_lm

Scale feature coverage values to estimate their absolute abundance
taxonomy.object

Taxonomy table in phyloseq format
DESeq2_l2fc

Calculating log2 fold change for HTS-SIP data.
df_atomX_boot

Bootstrapped atom fraction excess table
HRSIP

(MW-)HR-SIP analysis
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
calc_Mheavymax_MAGs

Calculate Mheavymax
as.Num

The following function is adapted from HTSSIP R package conversion to numeric
filter_na

Remove MAGs with NAs from atomX table
filter_l2fc

Filter l2fc table
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
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
phyloseq2df

The following function is adapted from HTSSIP R package phyloseq data object conversion to data.frame
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
atomX

Atom fraction excess table
f_tibble

Coverage table
GC_content

GC_content table
mag.table

MAG abundance table in phyloseq format
fractions

Fractions table
sample.table

phyloseq-styled sample table
samples.object

Fractions table in phyloseq format
tax.table

phyloseq taxa table from GTDB taxonomy input
phylo.qSIP

Master phyloseq object
incorporators_taxonomy

Isotope incorporator list with GTDB taxonomy
seq_dil

Sequins dilution table
sequins

Sequins table