armbrustlab Goto Github PK

armbrustlab.github.io

clusterpop

clusterPop is a R package that performs real-time clustering analysis and visualization of measured phytoplankton populations using a modified version of our software packge flowPhyto.

cruisereplay

Replay historical data feeds for a research cruise

cytdiv

cytoDiv is a R function that calculates ecological diversity indices for a microbial community based on its bio-optical properties measured at the single cell level by flow cytometry. The indices express the organization and structure of a community, its richness in physiological and genetic variations. The equations used to calculate the indices are described in Li, W. 1997 Limnology & Oceanography 42, 874:880

diel_eukaryotes

Code repository for 'Diel-regulated transcriptional cascades of microbial eukaryotes in the North Pacific Subtropical Gyre'

flowphyto

flowPhyto is a package for the R statistical programming language that uses automated computational methods (flowClust and flowMeans) to cluster phytoplankton populations, perform aggregate statistics and create maps of phytoplankton distribution from georeferenced flow cytometry data. For more details, see Ribalet, F., Schruth, D., and Armbrust, E.V. 2011. flowPhyto: enabling automated analysis of microsccopic algae from continuous flow cytometric data. Bioinformatics 27:732-733

global_thaps_clones

gradients-amplicon

Sharing is caring.

manta

Microbial Assemblage Normalized Transcript Analysis

marferret

Code repository for collection, ingestion, and processing of genomic and transcriptomic sequence data into a reproducible reference sequence database

matrix_model_matlab

Prepping SeaFlow data and using it in the Hunter-Cevera 2-population matrix growth model

moduledetection-evaluation

npac_euk_gene_catalog

North Pacific eukaryotic metatranscriptome assemblies and annotations

nwpac_amplicon

Workup of 16S/18S data from three cruises in the NW Pacific

opedia

seaflow-realtime-deployment

seaflow-transfer

SeaFlow data transfer tool

seaflowviz2

SeaFlow realtime data dashboard with Meteor

seaflowviz3

Web visualizations for SeaFlow data

seastar

SEAStAR is a package of tools supporting the construction of complete analysis pipelines for next-generation (Illumina®, SOLiD™) sequencing data generated from environmental samples.

sspopmodel_respiration

thaps_catl

trophic-mode-ml

Accompanying code for 'The dynamic trophic architecture of open-ocean protist communities revealed through machine-guided metatranscriptomics.'