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.