(pronounced /de.ko.de/) Robust Aitchison PCA for sparse omics datasets, linking specific features to beta-diversity ordination through the use of compositional biplots.
Gemelli is a toolbox for running tensor factorization on sparse compositional omics datasets. Gemelli performs unsupervised dimensionality reduction of spatiotemporal microbiome data. The output of gemelli helps to resolve spatiotemporal subject variation and the biological features that separate them.
Compositional differential abundance analysis. ALDEx2 provides a framework that encompasses essentially all high-throughput sequencing data types by modelling the data as a log-ratio transformed probability distribution rather than as counts.
`breakaway` is the premier package for statistical analysis of microbial diversity. `breakaway` implements the latest and greatest estimates of richness, as well as the most commonly used estimates. The `breakaway` philosophy is to estimate diversity, to put error bars on diversity estimates, and to perform hypothesis tests for diversity that use those error bars.
A qiime2 plugin supporting methods for geographic mapping of qiime2 artifact data or metadata.
Qiime2 plugin of COREMIC: CORE MICrobiome [https://doi.org/10.7717/peerj.4395]. This plugin works with qza files from QIIME 2.
Data augmentation is a very useful and widely used method in data science. Especially, it can increase the sample size of the training set for machine learning models. Rarefy for Augment uses a simple rarefaction method to achieve data augmentation. The data augmentation should only be implemented on the training data set.
QIIME 2 plugin for distribution-based clustering, which calls OTUs based on the similarity between their genetic sequences and their count distribution across samples.
Plugin for acquisition, re-use, and management of public nucleotide sequence (meta)data while adhering to open data principles.
The move from OTU-based to sOTU-based analysis, while providing additional resolution, also introduces computational challenges. We demonstrate that one popular method of dealing with sOTUs (building a de novo tree from the short sequences) can provide incorrect results in human gut metagenomic studies and show that phylogenetic placement of the new sequences with SEPP resolves this problem while also yielding other benefits over existing methods.
QIIME 2 plugin for calculating the Health Index from microbiome data. The plugin is based on the Gut Microbiome Health Index (GMHI) created by Gupta et al. 2020.
This plugin is wrapping `ili, for more information, see: https://github.com/MolecularCartography/ili.
ITSxpress trims the conserved flanking regions of of ITS sequences. ITSxpress is designed to support the calling of exact sequence variants rather than OTUs. This newer method of sequence error-correction requires quality score data from each sequence, so each input sequence must be trimmed. ITSxpress makes this possible by taking FASTQ data, de-replicating the sequences then identifying the start and stop sites using HMMSearch. Results are parsed and the trimmed files are returned.
QIIME 2 plugin for analysis of time series data, involving either paired sample comparisons or longitudinal study designs.
MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea, Eukaryotes, and Viruses) from metagenomic shotgun sequencing data with species-level resolution.
q2-micom provides an interface between Qiime 2 and MICOM. It allows you to create and simulate metagenome-scale metabolic community models and to predict metabolic fluxes taking place in a microbial consortium. It can incorporate abundance and environmental data.
q2-phylogenize allows users to link microbial genes to environments using phylogenetic regression. Phylogenetic regression takes into account the fact that species that share ancestry will often share phenotypic traits, including colonizing similar environments. This confounder can otherwise lead to high rates of spurious associations. We hope researchers who are doing functional analysis of 16S data will find this tool particularly useful.
Plugin to run the PICRUSt2 pipeline to get EC, KO, and MetaCyc pathway predictions based on 16S data. Either EPA-NG or SEPP can be used to place sequences into the required reference phylogeny.
QIIME2 plugin for generating the average rarefied table for library size normalization using repeated rarefaction. This simple "Average Rarefied Table" method has the potential to be an ideal alternative to the current one-shot rarefaction, as it can keep information and avoid variation of composition.
SCNIC (Sparse Cooccurence Network Investigation for Compositional data) is a tool for building correlation networks from feature tables, finding modules in said networks and summarizing those modules. Access to all these functionalities is available to qiime2 users via the q2-SCNIC plugin.
A QIIME 2 plugin wrapper for the SHOGUN shallow shotgun sequencing taxonomy profiler (https://github.com/knights-lab/SHOGUN).
Taxonomic resolution for marker gene molecules can be improved by encompassing longer sequences. The Short MUlitple Reads Framework algorithm allows the scaffolding of multiple marker gene regions against a reference database; this plugin allows the constructionof a database, reconstruction, and extends the algorithm and introduces a way to generate a corresponding phylogenetic tree following reconstruction.
REference Sequence annotation and CuRatIon Pipeline RESCRIPt is a QIIME 2 plugin to support a variety of operations for managing and curating reference sequence databases, DNA/RNA sequence data, and taxonomic data.