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advanced-vegan-webinar-july-2020

Delve deeper into using R and vegan to analyse complex multivariate community ecology data with this free webinar

amplicon-pipeline

Nguyen Lab's Amplicon Pipeline using QIIME2

amptk

AMPtk: Amplicon ToolKit for NGS data (formally UFITS)

animal_gut_16s-uni

artemis

Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation

barleymeta

scripts to reproduce the analysis and figures from Bulgarelli et al., 2015

co-occurrence

R scripts for performing co-occurrence analyses

comparison_of_da_microbiome_methods

cooc_compare

Supplementary code for co-occurrence analyses of Barner et al. (2018, Ecology) Appendices S1 and S2

csc-env-eff

Using CSC HPC environment efficiently training material

deicode

Robust Aitchison PCA from sparse count data

earth

edwebinar_mar19

Earthdata Webinar March 2019

f1000_workflow

flakaliden-2011

Flakaliden project 2011

fungal-trans

A Snakemake workflow for fungal metatranscriptomics

funguild

FUNGuild: parsing OTUs into functional guilds

githubtest

hpc-python

Python in High Performance Computing

intro-gam-webinar-2020

intro-vegan-webinar-july-2020

Get started using the vegan package for R for multivariate data analysis and community ecology

its_workflow

Repository to process ITS amplicon sequencing data and produce figures for Schneider et al (2021)

micropower

power estimation for microbiome studies analyzed with pairwise distances and PERMANOVA

nefi_microbe

office-microbes

Notebooks and code for our Sloan office microbiome project.

oueme-fungi-transect

Data and analysis for soil transect samples collected in Upper Ouémé Forest in Bènin in 2015-2016

reciprocal_smallest_distance

Reciprocal Smallest Distance (RSD) is a pairwise orthology algorithm that uses global sequence alignment and maximum likelihood evolutionary distance between sequences to accurately detects orthologs between genomes.

rnaseq

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

sangeranalyser

functions to analyse sanger sequencing reads in R

statistical-methods-seminar-series

Repository for code shared be presenters in the EFI hosted Statistical Methods Seminar Series