A set of functions to investigate raw data from (metabol)omics experiments intended to be used on a raw data matrix, i.e. following peak picking and signal deconvolution. Functions can be used to normalize data, detect biomarkers and perform sample classification. A detailed description of best practice usage may be found in the publication <doi:10.1007/978-1-4939-7819-9_20>.

Takes QC signal for each day and normalize metabolomic
    data that has been acquired in a certain period of time. At least
    three QC per day are required.

Contains functions that allow Bayesian meta-analysis (1) with binomial data, counts(y) and total counts (n) or, (2) with user-supplied point estimates and associated variances.   Case (1) provides an analysis based on the logit transformation of the sample proportion. This methodology is also appropriate for combining data from sample surveys and related sources. The functions can  calculate the corresponding similarity matrix. More details can be found in Cahoy and Sedransk (2023), Cahoy and Sedransk (2022)  <doi:10.1007/s42519-018-0027-2>, Evans and Sedransk (2001) <doi:10.1093/biomet/88.3.643>, and Malec and Sedransk (1992) <doi:10.1093/biomet/79.3.593>.

Meta-CART integrates classification and regression trees (CART) into meta-analysis. Meta-CART is a flexible approach to identify interaction effects between moderators in meta-analysis. The method is described in Dusseldorp et al. (2014) <doi:10.1037/hea0000018> and Li et al. (2017) <doi:10.1111/bmsp.12088>.

Clustering in metagenomics is the process of grouping of microbial contigs in species specific bins. This package contains functions that extract genomic features from metagenome data, find the number of clusters for that given data and find the best clustering algorithm for binning.

A set of tools for parsing, manipulating, and graphing data
    classified by a hierarchy (e.g. a taxonomy).

Functions to analyze coherence, boundary clumping, and turnover
    following the pattern-based metacommunity analysis of Leibold and Mikkelson
    2002  <doi:10.1034/j.1600-0706.2002.970210.x>. The package also includes 
		functions to visualize ecological networks, and to calculate modularity 
		as a replacement to boundary clumping.