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Age related changes in social integration with age in wild adult chimpanzees
PIME: A package for discovery of novel differences among microbial communities
Data and code for manuscript 'Phylogeny- and abundance- based metrics allow for the consistent comparison of core gut microbiome diversity indices across host species'. FRONTIERS IN MICROBIOLOGY 2021
SMETANA: a tool to analyse interactions in microbial communities
R and Stan code for: https://besjournals.onlinelibrary.wiley.com/doi/abs/10.1111/2041-210X.13072
Pstrain profiles strains in metagenomics data. It infers strain abundance and genotype for each species. Also, it has a single species mode; where given a BAM and VCF, it can phase the variants for…
analysis code for BayeTime manuscript on simulations and microbiome applications
A comprehensive and customizable R package for microbiome analysis.
An R package for data analysis in microbial community ecology
RAxML Next Generation: faster, easier-to-use and more flexible
A toolkit for analyzing and visualizing phylogenetic (placement) data
Massively parallel phylogenetic placement of genetic sequences
Statistical Rethinking course at MPI-EVA from Dec 2018 through Feb 2019
phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. …
Accurate sample inference from amplicon data with single nucleotide resolution
A repository for large-scale microbiome datasets, formatted for phyloseq
A package for designing compact and comprehensive capture probe sets.