workflows for offline analysis of 16S rRNA Nanopore data

Tools for visualising microbial community amplicon data

Create statistic summary of an Oxford Nanopore read dataset

Plotting scripts for long read sequencing data

A pipeline for metabarcoding fungi and other eukaryotes with full-length ITS sequenced with PacBio

Nextflow pipeline to analyze PacBio HiFi full-length 16S data

Deciphering microbial turnover along a gradient

biodiversity genomics course by Nicol Rueda, Karin Näsvall and Joana Meier from the Wellcome Sanger Institute

pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies basecaller (Albacore/Guppy)

Quality control for MinION sequencing data

Estimated marginal means

Ready-to-use pipeline to detect, count and identify the hgcAB genes, involved in mercury methylation, from metagenomes

Inference of microbial interaction networks from large-scale heterogeneous abundance data

A dynamic database of fungal trait measurements

Database and pipeline for phylogenetic determination of AMF from environmental sequences

Generalized Linear Mixed Model + Microbiome Regression-based Kernel Association Test (GLMM-MiRKAT)

Using R language in microbiome analysis

Statistical Rethinking Course for Jan-Mar 2023

Statistical Rethinking course at MPI-EVA from Dec 2018 through Feb 2019

Microbial ecological network visualization clustering

Materials for the STAMPS 2022 course at the MBL in Woods Hole, MA, USA

functions for analyzing phyloseq data

Pipe-friendly Framework for Basic Statistical Tests in R

Extract and Visualize the Results of Multivariate Data Analyses

R shiny app for interactive microbiome analysis

small RNA analysis programs: standalone jar files (sRNAbench, sRNAde, etc), manuals and Docker image

Barcode demultiplex for Illumina I1, R1, R2 fastq.gz files

R package for microbiome data visualization and statistics. Uses phyloseq, vegan and the tidyverse. Docker image available.