A comprehensive Galaxy workflow for the end-to-end analysis of transcriptomics data, featuring automated QC, clustering, spatial statistics, cell type annotation, and cell-cell communication.
Type: Galaxy
Creators: Amirhossein Naghsh Nilchi, Pavankumar Videm, Björn Grüning
Submitter: Amirhossein Naghsh Nilchi
POLY_PIPELINE
A data analysis pipeline for STOmics data tailored to polyploid organisms.
Contributing
Contributions are welcome! Please fork the repository and submit a pull request.
See the CONTRIBUTING.md for details.
Main Pipeline (Cluster Execution)
The core scripts are optimized for SGE and PBS clusters execution. They use relative paths and must be run from the POLY_PIPELINE main directory.
Data Input
The input file must be the ...
PaSTa is a nextflow-based end-to-end image analysis pipeline for decoding image-based spatial transcriptomics data. It performs imaging cycle registration, cell segmentation and transcripts peak decoding. It is currently supports analysis of three types of ST technology:
- in-situ sequencing-like encoding
- MERFISH-like encoding
- RNAScope-like labelling
Prerequisites:
- Nextflow. Installation guide: https://www.nextflow.io/docs/latest/getstarted.html
- Docker or Singularity. Installation guide: ...
