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MiscMetabar - Miscellaneous Functions for Metabarcoding Analysis

Facilitate the description, transformation, exploration, and reproducibility of metabarcoding analyses. 'MiscMetabar' is mainly built on top of the 'phyloseq', 'dada2' and 'targets' 'R' packages. It helps to build reproducible and robust bioinformatics pipelines in 'R'. 'MiscMetabar' makes ecological analysis of alpha and beta-diversity easier, more reproducible and more powerful by integrating a large number of tools. Important features are described in Taudière A. (2023) <doi:10.21105/joss.06038>.

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sequencingmicrobiomemetagenomicsclusteringclassificationvisualizationampliconamplicon-sequencingbiodiversity-informaticsecologyilluminametabarcodingngs-analysis

8.69 score 21 stars 2 dependents 126 scripts 353 downloads

cati - Community Assembly by Traits: Individuals and Beyond

Detect and quantify community assembly processes using trait values of individuals or populations, the T-statistics and other metrics, and dedicated null models. Provides tools to analyse 'intraspecific' trait variability and its consequences for community assembly. Implements a framework using individual-level trait data to decompose variance at the population, species, and community levels. Methods are described in 'Taudiere' and 'Violle' (2016) <doi:10.1111/ecog.01433>.

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4.80 score 13 stars 16 scripts 685 downloads

tidypq - Tidyverse-Style Verbs for Phyloseq Objects

Provides tidyverse-style verbs for manipulating phyloseq objects at four scales: samples, taxa, occurrences, and tree. Functions follow a consistent naming convention ({verb}_{scale}_pq) and support data masking for intuitive filtering, selection, and mutation operations.

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3.52 score 1 stars 11 scripts

greenAlgoR - Carbon Footprint Estimation for R Computations

Computes the carbon footprint and ecological impact of computational tasks in R. Based on the Green Algorithms framework (Lannelongue et al. 2021, <https://calculator.green-algorithms.org/>), this package provides functions to estimate energy consumption and CO2 emissions from R computations. It includes specialized support for targets pipelines and provides visualization tools for carbon footprint analysis. The package helps researchers and data scientists to measure the environmental impact of their computational work.

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3.00 score 1 stars 5 scripts

comparpq - An extension to {MiscMetabar} and {phyloseq} package to compare phyloseq object

Compare phyloseq object from the R phyloseq package. This package provides tools and functions to facilitate comparison and analysis of multiple phyloseq objects.

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2.75 score 1 stars 16 scripts

dbpq - Manage FASTA Reference Databases for Taxonomic Assignment

Download, format, summarize, and modify FASTA reference databases used for taxonomic assignment in metabarcoding pipelines. Supports major databases (UNITE, SILVA, PR2, BOLD, MaarjAM, Eukaryome) and converts between taxonomy header formats (dada2, SINTAX). Part of the 'pqverse' ecosystem.

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1.00 score 1 scripts