Computational Tools 

HyperCluster

A python package and SnakeMake workflow for parallelized clustering optimization. 

Github: https://github.com/liliblu/hypercluster

Documentation: https://hypercluster.readthedocs.io/en/latest/

Publication:

Blumenberg L, Ruggles KV. (2020) Hypercluster: a flexible tool for parallelized unsupervised clustering optimization BMC Bioinformatics

Python version:

• Github: https://github.com/ruggleslab/blackSheep

• PIP: https://pypi.org/project/blksheep/

• Bioconda: https://bioconda.github.io/recipes/blksheep/README.html

R version:

• Github: https://github.com/ruggleslab/blackSheepR

• Bioconductor: https://bioconductor.org/packages/release/bioc/html/blacksheepr.html

Publication:

Blumenberg L, Kawaler E., Cornwell M, Smith S, Ruggles KV, Fenyo D. (2019) BlackSheep: A Bioconductor and Bioconda package for differential extreme value analysis. bioRxiv 825067

Workflow Hub for Automated Metagenomic Exploration (WHAM!)

WHAM!

Rshiny web-tool allowing for exploratory analysis of metagenomics and metatranscriptomic data.  Includes visualization and statistical analysis on the gene family and taxa level. 

Publication:

Devlin JC, Battaglia T, Blaser MJ, Ruggles KV. (2018) WHAM!: a web-based visualization suite for user-defined analysis of metagenomic shotgun sequence data. BMC Genomics. PMID: 29940835