Hematokytos

Hematokytos ("blood cell") collects pipelines and utilities for gathering, integrating, and analysing single-cell data from direct reprogramming experiments alongside native hematopoietic cell types. Workflows cover preprocessing, quality control, RNA velocity, and network analysis with a focus on hematopoietic stem and progenitor cells.

Repository Structure

• pipelines/ – Collection of workflow scripts
  • cc_pipeline/ – Nextflow pipeline for cell cycle samples
  • bm_pipeline/ – Nextflow pipeline for bone marrow data
  • hsc_pipeline/ – Nextflow pipeline for direct reprogramming experiments
  • velocyto_pipeline/ – Snakemake workflow for running Velocyto
  • DeepCycle/ – Scripts to run the DeepCycle model
  • CABYBARA/ – Capybara cell identity assignment scripts
  • scMINER/ – Network inference with SJARACNe
• notebooks/ – Jupyter notebooks for exploratory analysis and figure generation (see notebooks/README.md for an overview)
• reference_atlas/ – Scripts for collecting and annotating reference datasets
• resources/ – Gene sets, metadata and supporting files
• NextCell/ – Exploration of the NextCell algorithm
• results/ – Example output tables
• utils/ – Small helper modules

Each pipeline directory contains its own README with usage instructions.