CellularHeatmaps

CellularHeatmaps github repository contains all the necessary code to reproduce the models and analysis in [CITE PAPER].

Pipeline -- Nextflow

On thalassa

1. Generate labels with the given folder

'bash script/thalassa_fab_tnbc.sh'

'bash script/thalassa_substrat.sh'

'bash script/thalassa_label.sh

bash script/thalassa_umap.sh

bash script/thalassa_classification_U2MAP_8.sh '

Cellular Segmentation

The first cellular segmentation model

Project nature: TNBC (Fabien + Substrat)

After generating the labels:

1. 0_data_prep.sh
2. 1_umap_generation.sh
3. 2_classification.sh

TODO

• fix name out of repositioning, there is a trailing r in the name.
• documentation
• test
• requirements
• filter all patients
• extra files are annoying
• check it runs
• evaluation
• plots