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    24 repositories

    • KEGGDecoder-heatmap

      Public
      metabolic heatmap
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •10•0•0•0•Updated Nov 1, 2019Nov 1, 2019

    • speeding-up-science-workshops.github.io

      Public
      Repository with materials for the Speeding Up Science Workshops at UC Davis
      Python
      •8•9•0•0•Updated Oct 31, 2019Oct 31, 2019

    • metabarcode-SUS-Tree

      Public
      Building an interactive phylogenetic tree
      R
      •1•0•0•0•Updated Oct 31, 2019Oct 31, 2019

    • 16s-interactive-tree

      Public
      replaced by metabarcode-interactive-tree
      R
      •
      GNU General Public License v3.0
      •1•1•0•0•Updated Oct 31, 2019Oct 31, 2019

    • MetaG-MAG-representation

      Public
      An alternative Binder to MetaG-heat-Binder that should only work with a .Rmd input file.
      HTML
      •
      MIT License
      •2•0•0•0•Updated Oct 31, 2019Oct 31, 2019

    • speeding-up-sci-correlation

      Public
      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.
      Jupyter Notebook
      •
      MIT License
      •1•0•0•0•Updated Oct 31, 2019Oct 31, 2019

    • MetaT-taxa-and-function-summary

      Public
      HTML
      •
      MIT License
      •1•0•0•0•Updated Oct 31, 2019Oct 31, 2019

    • Heat-Tree

      Public
      heat tree visualization
      HTML
      •2•0•0•0•Updated Oct 31, 2019Oct 31, 2019

    • Abundance_barplot

      Public
      HTML
      •1•0•0•0•Updated Oct 31, 2019Oct 31, 2019

    • Metabarcoding_viz

      Public
      R
      •1•0•0•0•Updated Oct 31, 2019Oct 31, 2019

    • ord_abund_raretaxa

      Public
      Workflow using phyloseq and CRT function to identify, calculate, and visualize relative abundances and ordination of conditionally rare taxa
      R
      •2•0•0•0•Updated Oct 31, 2019Oct 31, 2019

    • Metabarcoding_TARA_Oceans_TimeSeries

      Public
      Example of visualisations and analysis using a short time series available from Tara Oceans
      R
      •1•0•0•0•Updated Oct 30, 2019Oct 30, 2019

    • metabarcoding_alphaviz

      Public
      R
      •0•0•0•0•Updated Oct 25, 2019Oct 25, 2019

    • relativeabundance_crt

      Public
      Speeding Up Science Hackathon 2019 workflows
      HTML
      •1•0•0•0•Updated Oct 25, 2019Oct 25, 2019

    • metabarcode-random-forest

      Public
      example diversity analyses for fecal microbiome transplant dataset
      R
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Oct 25, 2019Oct 25, 2019

    • metabarcode-NMDS

      Public
      NMDS plots from metabarcoding data
      R
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Oct 25, 2019Oct 25, 2019

    • MAGstats-binder

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Oct 25, 2019Oct 25, 2019

    • metabarcode-first-look-viz

      Public
      Code for the metabarcoding group with the UCDavis Speeding up science Hackathon
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Oct 25, 2019Oct 25, 2019

    • MetaG-heat-Binder

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Oct 25, 2019Oct 25, 2019

    • metatranscriptomics-visualizations

      Public
      HTML
      •3•0•0•0•Updated Oct 25, 2019Oct 25, 2019

    • metaT-LDA-analysis

      Public
      R
      •2•0•0•0•Updated Oct 25, 2019Oct 25, 2019

    • Heatmap

      Public
      Example of a basic heatmap using ggplot2
      HTML
      •1•0•0•0•Updated Oct 25, 2019Oct 25, 2019

    • abundance-viz-metabarcoding

      Public
      R
      •1•1•0•0•Updated Oct 25, 2019Oct 25, 2019

    • speeding-up-science

      Public
      0•0•0•0•Updated Oct 24, 2019Oct 24, 2019