Repository with pipelines and utilities for gathering, integrating, and analyzing single-cell RNA sequencing data from transcription factor (TF) perturbation experiments. Datasets include one control condition (normal proliferating human fibroblasts) and three perturbation conditions: MYOD1 overexpression (OE), PRRX1 knockdown (KD), and sequential PRRX1 KD / MYOD1 OE. Current workflows cover preprocessing and quality control. The repository will be updated as the project is ongoing.
pipelines/- Collection of workflow scriptsEPI2ME/- Nextflow pipeline for TF perturbation experiments
notebooks/- Jupyter notebooks for exploratory analysis and figure generation (seenotebooks/README.mdfor an overview)resources/- Gene sets, metadata, and supporting files
Each pipeline directory contains its own README with usage instructions.