Batch effect correction. Implementing function run_bbknn()
Hello, this is a calling to implement the function to run the batch effect correction using the bbknn
1. The codes for this function is here (author: Fatemeh): /mnt/agnerds/loosolab_SC_RNA_framework/03_RNA_pul40+pul49_batch_correction.ipynb
2. The general idea where this function is located in the workflow is here: Notebook 3 Overview https://intranet.mpi-bn.mpg.de:8443/display/Bioinf/Notebook+3%3A+Normalization%2C+correction%2C+comparisons
3. This new function should be located in the analyser.py module
Please, take a look in thee manual of bbknn before coding to see the requirements to execute this program (e.g., normalisations, so on). Then, implement the codes to provide these requirements inside this function if needed.
Edited by guilherme.valente