Analysis Scripts & Pipelines

This section contains the core computational notebooks and scripts used for data processing, statistical analysis, and visualization.

Preprocessing & Guide Calling

• Guide Calling for Dual Guides
• Filtering for Cells with Ideal Combination of Guides
• Guide Calling Using the Cellranger Module HDF5 File

Additional Files:

• Shell Pipeline: 1_cellranger.sh

Transcript Quantification

• Whippet Pseudobulk Analysis

Additional Files:

• Shell Scripts: 3A_seperate_bam_file_ideal.sh | 3B_whippet_pseudobulk.sh

Transcriptional Divergence (E-Stats & Differential Expression)

• E-distance of P1 and P2 Knockdown
• Target gene and neighbouring gene expression
• Quantitative individual UMAPs per gene of interest
• Differential Expression analysis between P1 & P2

Cell Phase & Pathway Modeling

• Cell Assignment Model from FUCCI-Matched Single-Cell Paper
• Investigating Copy Number Variation Across KD Populations
• Velocity and pyGSEA calculations of ESR1
• Investigating Gene Pathway Enrichment with Spectra

Clinical & Promoter Prevalence

• Survival Curve Isoform Analysis