This code repo hosts scripts and analysis protocols used to generate results that are reported in our study:

Yao, L. et al. High-resolution reconstruction of cell-type specific transcriptional regulatory processes from bulk sequencing samples. Preprint at bioRxiv (2025).

Structure of this repo

Protocols

This folder stores major protocols/pipelines that we used to analyze/simulate sequencing data. Files are in json format; they are structured as follows:

• name
• description
• step: a list of steps in this protocol/pipeline
  • step_order: the order of this step in the protocol
  • software: software used
  • parameter: parameters for the software
  • version_check: how to report the version of the software
• reference: a dictionary of predefined variables that are referred to in this protocol
  • key: name of the reference
  • value: description about this reference

Analysis

Scripts that we used to analyze data generated from protocols and produce aggregated files for downstream plotting.

Software

In house scripts and modifications to published tools to incorporate them into our pipeline.