https://github.com/novartis/pisces

PISCES is a pipeline for rapid transcript quantitation, genetic fingerprinting, and quality control assessment of RNAseq libraries using Salmon.
https://github.com/novartis/pisces

bioinformatics bioinformatics-pipeline rnaseq rnaseq-pipeline salmon transcriptomics

Last synced: 3 months ago
JSON representation

PISCES is a pipeline for rapid transcript quantitation, genetic fingerprinting, and quality control assessment of RNAseq libraries using Salmon.

• Host: GitHub
• URL: https://github.com/novartis/pisces
• Owner: Novartis
• License: apache-2.0
• Created: 2020-11-30T21:33:50.000Z (almost 5 years ago)
• Default Branch: master
• Last Pushed: 2025-06-17T17:07:41.000Z (4 months ago)
• Last Synced: 2025-07-20T17:55:27.504Z (3 months ago)
• Topics: bioinformatics, bioinformatics-pipeline, rnaseq, rnaseq-pipeline, salmon, transcriptomics
• Language: Python
• Homepage:
• Size: 17.6 MB
• Stars: 30
• Watchers: 1
• Forks: 3
• Open Issues: 12
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

README

          
[![CI](https://github.com/Novartis/pisces/workflows/CI/badge.svg)](https://github.com/Novartis/pisces/actions?query=workflow%3ACI)

[![Sphinx Docs](https://github.com/Novartis/pisces/workflows/Sphinx%20Docs/badge.svg)](https://opensource.nibr.com/pisces/)

[![Package Builds](https://github.com/Novartis/pisces/workflows/Package%20Builds/badge.svg)](https://github.com/Novartis/pisces/actions?query=workflow%3A%22Package+Builds%22)

[![PyPI](https://badge.fury.io/py/novartis-pisces.svg)](https://pypi.python.org/pypi/novartis-pisces)

# PISCES: a package for quantitation and QC of large scale mRNA-seq datasets

PISCES is a pipeline for rapid transcript quantitation, genetic fingerprinting, and quality control assessment of RNAseq libraries using Salmon.

See the current documentation at https://opensource.nibr.com/pisces/. Read the manuscript at https://www.biorxiv.org/content/10.1101/2020.12.01.390575v1.

Matthew D Shirley, Viveksagar K Radhakrishna, Javad Golji, Joshua M Korn. (Preprint) PISCES: a package for rapid quantitation and quality control of large scale mRNA-seq datasets. bioRxiv. 2020.

## Quickstart

Installation:

```

$ pip install --user novartis-pisces

$ pisces_dependencies

```

Submitting jobs to an HPC cluster:

```

$ pisces submit -m metadata.csv

```

Summarizing QC metrics and gene expression:

```

$ pisces summarize-qc -m metadata.csv -f fingerprint.txt

$ pisces summarize-expression -m metadata.csv

# optionally specify contrasts and formula for DESeq2 differential gene expression

$ pisces summarize-expression -m metadata.csv -f contrasts.csv -d "~covariate1 + covartiate2"

```

Please submit bugs or questions to our issue tracker.