Pinned Repositories
armbrustlab.github.io
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
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
marferret
Code repository for collection, ingestion, and processing of genomic and transcriptomic sequence data into a reproducible reference sequence database
NPac_euk_gene_catalog
North Pacific eukaryotic metatranscriptome assemblies and annotations
seaflow-realtime-deployment
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.
trophic-mode-ml
Accompanying code for 'The dynamic trophic architecture of open-ocean protist communities revealed through machine-guided metatranscriptomics.'
Armbrust Lab's Repositories
armbrustlab/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.
armbrustlab/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
armbrustlab/seaflowviz2
SeaFlow realtime data dashboard with Meteor
armbrustlab/armbrustlab.github.io
armbrustlab/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
armbrustlab/marferret
Code repository for collection, ingestion, and processing of genomic and transcriptomic sequence data into a reproducible reference sequence database
armbrustlab/seaflow-realtime-deployment
armbrustlab/trophic-mode-ml
Accompanying code for 'The dynamic trophic architecture of open-ocean protist communities revealed through machine-guided metatranscriptomics.'
armbrustlab/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.
armbrustlab/NPac_euk_gene_catalog
North Pacific eukaryotic metatranscriptome assemblies and annotations
armbrustlab/seaflow-transfer
SeaFlow data transfer tool
armbrustlab/seaflowviz3
Web visualizations for SeaFlow data
armbrustlab/cruisereplay
Replay historical data feeds for a research cruise
armbrustlab/diel_eukaryotes
Code repository for 'Diel-regulated transcriptional cascades of microbial eukaryotes in the North Pacific Subtropical Gyre'
armbrustlab/global_thaps_clones
armbrustlab/gradients-amplicon
Sharing is caring.
armbrustlab/manta
Microbial Assemblage Normalized Transcript Analysis
armbrustlab/matrix_model_matlab
Prepping SeaFlow data and using it in the Hunter-Cevera 2-population matrix growth model
armbrustlab/moduledetection-evaluation
armbrustlab/NWPac_amplicon
Workup of 16S/18S data from three cruises in the NW Pacific
armbrustlab/opedia
armbrustlab/ssPopModel_respiration
armbrustlab/Thaps_Catl