Table of Contents

  1. Overview of Galaxy-ME histories
  2. Manuscript history ID table
  3. Galaxy-ME Tutorials
  4. Primary Data Access

Overview of Galaxy-ME Histories

Each dataset analyzed in this study has an analysis history on cancer.usegalaxy.org under the published histories tab. The Galaxy histories contain the images which can be viewed using Avivator or Vitessce, all analysis steps, parameters used, and additional files (marker files, phenotype workflows, GMM threshold plots, etc.). The histories can be imported into a user’s own personal history to re-run the analysis or run additional GalaxyME tools on the datasets.

Screenshot of published histories page

Manuscript history ID Table

History Manuscript ID History Name
Tonsil 1 GalaxyME_SARDANA_Tonsil_CycIF_2024
Tonsil 2 GalaxyME_SARDANA_Tonsil_mIHC_2024
Tonsil 3 GalaxyME_SARDANA_Tonsil_CODEX_2024
Tonsil 4 GalaxyME_SARDANA_Tonsil_combined_assay_analysis_2024
Tonsil 5 GalaxyME_SARDANA_Tonsil_CycIF_Extended_2024
Tonsil 6 GalaxyME_SARDANA_Tonsil_CELESTA_2024
CRC 1 GalaxyME_SARDANA_CRC_mIHC_2024
CRC 2 GalaxyME_SARDANA_CRC_CycIF_Visinity_2024

This table provides a shorthand ID so that histories can be referenced in the manuscript methods

Galaxy and Galaxy-ME tutorials

For a general introduction to navigating and performing analyses in Galaxy, see the Galaxy Training Network’s Introductory Tutorials [1,2].

For an example and tutorial of a Galaxy-ME workflow, see End-to-End Tissue Microarray Image Analysis with Galaxy-ME

Primary Data Access

All of the original files and information about the analyses conducted for the MCMICRO study can be found in this Synapse folder.

The SARDANA CRC data analyzed in this study can be found in this Synapse folder.

References

  1. Saskia Hiltemann, Nicola Soranzo, Clemens Blank, Anton Nekrutenko, Björn Grüning, Anne Pajon, Helena Rasche, 2022 Galaxy 101 (Galaxy Training Materials).https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-101/tutorial.html Online; accessed Fri Jul 08 2022
  2. Batut et al., 2018 Community-Driven Data Analysis Training for Biology Cell Systems 10.1016/j.cels.2018.05.012