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mcr-metag-frenemies

meta-eukomic

microbes-need-frenemies-euk-metat

Descriptions and code for metatranscriptome analysis related to project "Microbes need frenemies"

microcolonizers-gordaridge

microeuk-amplicon-survey

Globally-distributed microbial eukaryotes exhibit endemism at deep-sea hydrothermal vents

midcayman-rise-microeuk

Data analysis for Microbial eukaryotic predation pressure and biomass at Mid-Cayman Rise: Implications for deep-sea carbon cycling

pacificocean-metat

paiges_dissertation_poster

Original, totally real, & not fake raw data to make Paige's dissertation poster

palettewoodshole

R color palettes inspired by Woods Hole and Falmouth.

phylogeny-r-amplicon

prelim-figures-intro-r

Introduction to using R to compile, analyze, and interpret tag-sequencing data.

preliminaryfigures_v4_tagseq

Tutorial to generate preliminary figures from an OTU table. Example figures to give you a first look at your data!

protist-gordaridge-2019-analysis

Data analysis and code associated with study of microbial eukaryotes at Gorda Ridge hydrothermal vent field

protist-gordaridge-2021

Data analysis, raw data, and Rmarkdown files for protist grazing paper.

qc-trim

snakemake pipeline to quality check and trim .fastq reads

qiime2-2024

qiime2_asvworkflow_v8

r-microbio-ocean

r-novice-gapminder

R for Reproducible Scientific Analysis

r-ventures

rain_analysis_example

Using an OTU table as test data, this script demonstrates suggested normalization and detrending steps ahead of RAIN analysis to detect rhythms in time-series data

sarah-hu

sarahkhu-cv

shiny-wordle

Wordle in Shiny

slo-pier-comparison-2023

slo-pier-weekly

snake-metag

spot_metatranscriptome

Required code for data compilation and analysis for a eukaryotic-focused metatranscriptome survey in the North Pacific.

swarm

A robust and fast clustering method for amplicon-based studies

tagseq-qiime2-snakemake

Pipeline to run qiime2 with snakemake