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Phase I (theoretical) & Phases II (practical) schedules

Phases II Schedule

The aim of the practical workshops will be to explore different aspects of high-content cytometry data analysis with experts in the field, and to train young researchers for future implementation in their practice. The principle, the workflow, interpretation and comparison of each process/tool will be discussed.

For the participants of the practical workshops 1 and 4, a good experience in conventional data analysis is required. For workshop 1, experience of FlowJo and unsupervised analysis is required. For the workshops 2 and 3, a minimal level of experience in R will be required.

Workshop 1- Control and push the limits of unsupervised analysis (3 effective days, 2 nights on site, starting from 14:00 the first day, ending at noon the last day).

1. Recap of Quality Control, Intensity Transformation and Batch Effect (including a recap of an unsupervised analysis pipeline)
2. Transforming intensity: impact on dimension reduction and clustering
3. Data cleaning using FlowAI, PeacoQC and FlowCut algorithms: comparison and parameters optimization with different datasets
4. Correcting batch effects using CytoNorm, CyCombine and CytoBatchNorm: with or without reference sample, correction check
5. Recap of Cell Annotation
6. Annotating cells using Scyan and Scaffold: comparison to heatmap, ClusterExplorer and MEM
7. Addressing large experiments with FlowSOM and by up-sampling with Embded and kNN.

Workshop 2- Dimension reduction and clustering pipelines and available tools (3 effective days, 2 nights on site, starting from 14:00 the first day, ending at noon the last day).

1. Introduction to dimension reduction and clustering pipelines - 1h (day 1 pm)
2. OmiQ presentation and manipulation - 1h + 2h (day 1 pm)
3. Cytobank presentation and manipulation - 1h + 2h (day 2 am)
4. Cytolitics presentation and manipulation - 1h + 2h (day 2 pm)
5. cytofkitlab R package GUI manipulation - 1h (day 3 am)
6. cytofkitlab R package script manipulation - 3h (day 3 am)

Workshop 3- Automated supervised pipelines with OpenCyto and FowDensity (3 effective days, 2 nights on site, starting from 14:00 the first day, ending at noon the last day).

1. Introduction to automatic gating and available pipelines - 1h (day 1 pm)
2. Flowdensity package presentation and manipulation - 3h (day 1 pm)
3. OpenCyto package presentation and manipulation - 3h (day 2 am)
4. OpenCyto automatic pipeline construction - 3h (day 2 pm)
5. Validation and evaluation of results using manual gating - 1h (day 2 pm)
6. Advance manipulation of OpenCyto and FlowDensity scripts for full automatization - 3h (day 3 am) 

Workshop 4- Full analysis pipeline supported by Business Intelligence tools (3 effective days, 2 nights on site, starting from 14:00 the first day, ending at noon the last day).

1. Panel Design
2. Manual hierarchical analysis
3. Automatic unsupervised analysis (clustering and dimension reduction)
4. Metadata integration
5. Statistical analysis
6. Database building and visualization (integration of information generated from steps 1 to 5 in a unique database)
7. Table Public sharing (including Ethical aspects of Patient data sharing)