Zavolab
Published March 6, 2024 | Version v1.0.0-rc.1
Software Open

ZARP-cli: A user-friendly command-line interface for the ZARP RNA-seq analysis workflow

Creators

  • 1. ROR icon University of Basel
  • 2. ROR icon SIB Swiss Institute of Bioinformatics

Description

💊 ZARP - RNA-Seq analysis made easy! 💉

  • You have a bunch of RNA-Seq samples and wanna know what's in them?   ZARP 'em!
  • You have an extensive SRA query with hundreds of runs and you don't know where to start?   Easy - ZARP 'em!
  • Barry left you some samples to analyze and then went on vacation, again?   No problem, ZARP 'em!

ZARP-cli uses the HTSinfer package to infer missing metadata and then runs the ZARP - the Zavolab Automated RNA-seq Pipeline on your samples. Impress your colleagueswith your sudden productivity boost. Or better yet, use the time saved to go on that camping trip with Barry. Just make sure to guard your secret! 😉

Notes

MK and MBak  were supported by the "Biozentrum PhD Fellowships" program.

Files

zavolanlab/zarp-cli-v1.0.0-rc.1.zip

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Additional details

Related works

Is supplement to
Software: https://github.com/zavolanlab/zarp-cli (URL)

Funding

NCCR RNA & disease: The role of RNA biology in disease mechanisms (phase II) 182880
Swiss National Science Foundation
Cell type-specific expression of 3’ untranslated region isoforms: quantification, modeling, and prediction of functional impact 189063
Swiss National Science Foundation

Software

Repository URL
https://github.com/zavolanlab/zarp-cli
Programming language
Python
Development Status
Active