pSigOmics

NFkB pSigOmics

This repository contains code for the manuscript "High Throughput, Programmable Fixation Reveals the RNA and protein co-regulation with Spatially Resolved NFκB Pseudo-signaling". Codes are run under the specified Anaconda environment.

To set up environments, run the following command: conda env create -f environ.yml

Example data can be found at: https://zenodo.org/records/11292144

01_dim_reduce_2D_embedding_drug_vs_control.ipynb creates the plot for single cell latent space embeddings (Fig. 4b)

02_boxplot_p65_stim_continuous_drug_vs_control.ipynb plots the RNA and protein curves over this time axis to illustrate the anticorrelation effect.

We also investigated the relationship between p65 RNA (signaling) and GAPDH RNA (signaling)

03_scatterTimePoints_RNA_protein_drug_vs_control plots the NFkB response across static fixation times.

And also computes the $R^2$ correlation between p65 RNA and protein at each static fixation time

Citation

Please cite: TBD