hurwitzlab/planet-microbe-datapackages

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hurwitzlab/planet-microbe-datapackages

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Data packages for the Planet Microbe project

elm-imicrobe-spa

docker-mothur

Docker image for running mothur.

biosys-analytics

BE434/535 Biosystems Analytics

appetizer

Create the app.json for Stampede

planet-microbe-functional-annotation

gnu-parallel-yourself

Template script and instructions for using GNU Parallel in place of the TACC Launcher on Stampede2.

WGCNA-of-Type-II-Diabetic-Skin

WGCNA of Type II Diabetic Skin

phage_detection_benchmarks

Code used to benchmark metagenomic phage detection tools.

orminator

Generate SQLAlchemy ORM classes for an existing database.

singularity-phispy

Singularity container for phispy

bacteria-bowtie

Simple bioinformatics pipeline to align / count RNA reads to a bacterial genome with bowtie2 / cuffnorm and cuffquant

imicrobe-lib

General purpose scripts and libraries for iMicrobe.

centrifuge-filter

Use Centrifuge calls to filter sequence (FASTA) into accepted/rejected

imicrobe-mash-node2vec

Scripts to learn and cluster a vector-space embedding on all-vs-all iMicrobe MASH distance matrix.

centrifuge

Run Centrifuge on Stampede

elm-imicrobe-search

node-imicrobe

Node app server for iMicrobe data

ivirus-mojo

Mojo for iVirus

biosystems-analytics-2020

434/534 Biosystems Analytics course at the University of Arizona

meowl

Microbial Environments described using OWL (MEOWL)

Web Ontology Language

fizkin

All-vs-all sequence comparison for WGS

kmerizer

Working with k-mers

mash

viral-learning

Deep learning demonstration code.

planet-microbe-app

Planet Microbe - Semantic search across ‘omics, environmental, and physiochemical data layers.

Host-Screen

Utilizes Bowtie2 to remove host contaminated read from Fasta/q files