Welcome to cancer.usegalaxy.org!

The Cancer Galaxy serves as a hub for tools commonly used in analysis of cancer datasets. This server currently features tools for: Multiplex Tissue Imaging with Galaxy-ME, QIIME2, IOBIO Interactive tools, and machine learning with Galaxy-ML. This server is a collaborative effort and we welcome any suggestions or requests for making tools related to cancer analysis available on this server. We also welcome contributions to the development of new tools, workflows or trainings!



Getting Started

Are you new to Galaxy, or returning after a long time, and looking for help to get started? Take an interactive tour:

Galaxy UI History Scratchbook

Tools Suites available

Galaxy-ME

Tools

All of the Galaxy tools for MCMICRO have been developed by the Goecks lab at the Moffitt Cancer Center and the Oregon Health and Science University.

Tool Description Reference
basic_illumination BaSiC shading correction for use with Ashlar Peng et al. 2017
ashlar ASHLAR: Alignment by Simultaneous Harmonization of Layer/Adjacency Registration Muhlich et al. 2021
coreograph Dearray of Tissue Microarrays Coreograph Github
unmicst UnMICST - Universal Models for Identifying Cells and Segmenting Tissue UnMICST info
s3segmenter S3segmenter: Generates single cell (nuclei and cytoplasm) label masks S3Segmenter github
quantification MCQuant: Single cell quantification MCQUant github

Tutorials and Workflows

A Hands-on Galaxy-ME Tutorial highlights an example analysis of a tissue microarray. Two workflows are currently available to process your samples using the MCMICRO Galaxy pipeline:

MCMICRO Tissue Microarray Workflow

MCMICRO Whole Slide Tissue Workflow

Contributors

Galaxy is an open platform for supporting data intensive research. Galaxy is developed by The Galaxy Team with the support of many contributors.