Computational Tools 

 

BlackSheep

A tool for differential extreme-value analysis with packages in both Python and R. Publication to come!

Python : https://github.com/ruggleslab/blackSheep

R : https://github.com/ruggleslab/blackSheepR

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Workflow Hub for Automated Metagenomic Exploration

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. 

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


Ribosomal Investigation and Visualization to Evaluate Translation

RIVET

A simple to use tool to automate the statistical analysis of RNA seq data acquired from polysome profile or ribosome footprinting experiments.

Ernlund A, Schneider R, Ruggles KV. RIVET: comprehensive graphic user interface for analysis and exploration of genome-wide translatomics data. (2018). BMC Genomics.

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