speeding-up-science-workshops

speeding-up-science-workshops.github.io

Repository with materials for the Speeding Up Science Workshops at UC Davis

16s-interactive-tree

replaced by metabarcode-interactive-tree

abundance-viz-metabarcoding

Abundance_barplot

Heat-Tree

heat tree visualization

KEGGDecoder-heatmap

metabolic heatmap

metabarcode-SUS-Tree

Building an interactive phylogenetic tree

Metabarcoding_TARA_Oceans_TimeSeries

Example of visualisations and analysis using a short time series available from Tara Oceans

Metabarcoding_viz

MetaT-taxa-and-function-summary

metatranscriptomics-visualizations

ord_abund_raretaxa

Workflow using phyloseq and CRT function to identify, calculate, and visualize relative abundances and ordination of conditionally rare taxa

relativeabundance_crt

Speeding Up Science Hackathon 2019 workflows

speeding-up-sci-correlation

Visualization codes from the 2nd "speeding up science workshop". This repository contains codes to plot and calculate correlation (linear regression) between metagenomic and metatranscriptomic sequencing results acquired from the same sample.

speeding-up-science

Heatmap

Example of a basic heatmap using ggplot2

MAGstats-binder

metabarcode-first-look-viz

Code for the metabarcoding group with the UCDavis Speeding up science Hackathon

metabarcode-NMDS

NMDS plots from metabarcoding data

metabarcode-random-forest

example diversity analyses for fecal microbiome transplant dataset

metabarcoding_alphaviz

MetaG-heat-Binder

MetaG-MAG-representation

An alternative Binder to MetaG-heat-Binder that should only work with a .Rmd input file.

metaT-LDA-analysis