Add CPJUMP1 buscar MoA Analysis Notebooks

[axiomcura]

This PR introduces a series of Jupyter notebooks and supporting scripts for the cpjump1-analysis pipeline, focusing on Mechanism of Action (MoA) analysis for the CPJUMP1 dataset. The notebooks guide users through the process of generating on/off signatures, assessing heterogeneity, calculating on/off scores, and running MoA-based compound ranking analyses.

Key Additions

• 1.generate-on-off-signatures.ipynb: Generates on/off gene expression signatures for compounds in the CPJUMP1 dataset.
• 2.assess-heterogeneity.ipynb: Assesses phenotypic heterogeneity across compound treatments.
• 3.calculate-on-off-scores.ipynb: Calculates on/off scores to quantify compound activity.
• 4.run_buscar_rankings_base_on_moa.ipynb: Runs compound ranking analyses based on MoA annotations.
• 5.cpjump_u2os_MoA_analysis.ipynb: Performs detailed MoA analysis for U2OS cell line data, including data integration, visualization, and result interpretation.

Other files:

• run-cpjump1-buscar-analysus.sh: Shell script to automate the analysis pipeline.
• nbconverted/: Contains Python scripts converted from the notebooks for reproducibility and batch execution.
• plots/ and results/: Output directories for generated figures and result files.

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[wli51]

The bulk of the shuffling analysis LGTM. I think I have found the PRC bug that needs to be fixed to yield normal plots, please see comments under notebooks/4.cpjump1-analysis/nbconverted/5.cpjump_u2os_MoA_analysis.py.

[axiomcura]

Thanks for the review @wli51 I have created issues and attended some of the bugs that were found here. Thank you for your through review!