The drake R package
The drake R package: a pipeline toolkit for reproducibility and high-performance computing - Published in JOSS (2018)
The targets R package
The targets R package: a dynamic Make-like function-oriented pipeline toolkit for reproducibility and high-performance computing - Published in JOSS (2021)
VeridicalFlow
VeridicalFlow: a Python package for building trustworthy data science pipelines with PCS - Published in JOSS (2022)
Python class defining a machine learning dataset ensuring key-based correspondence and maintaining integrity
Python class defining a machine learning dataset ensuring key-based correspondence and maintaining integrity - Published in JOSS (2017)
Baargin
Baargin: a Nextflow workflow for the automatic analysis of bacterial genomics data with a focus on Antimicrobial Resistance - Published in JOSS (2023)
cutandrun
Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes QC, support for spike-ins, IgG controls, peak calling and downstream analysis.
hotsub
hotsub: A batch job engine for cloud services with ETL framework - Published in JOSS (2018)