hadaca3_framework

A framework to collectively develop multi-omic deconvolution methods.

The framework contains several blocks

• pre-processing :
• feature_selection :
• split :
• deconvolution :
• early_int :
• late_int :
• intermediate_int :

## Environnement

Set up your conda environement as follow:

conda create -y -n hadaca3framework_env
conda activate hadaca3framework_env

mamba install -y  -c bioconda -c conda-forge -c r snakemake python r-base r-rmarkdown r-nnls r-seurat

Retrieve data.

Download data from:

Execute the pipeline:

To run the pipeline:

1. Set the envionnement with the code above
2. Retrieve the data
3. Execute order 66 ! (snakemake --cores 4 -s 00_run_pipeline.py -p)

mkdir 00_demo_data
#then copy in it starting_kit_phase2-3/data

### TODO

• Set a file format to use :
  • feather ?
  • parquest ? ...
• Pre-processing return a multi data that contains ref and mix but only change ref ?