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clockSim - Streamlined Simulation of Circadian Gene Networks

A user-friendly workflow for simulating circadian clock gene networks. Despite decades of advances in modeling circadian clock dynamics, the lack of accessible tools for reproducible simulation workflows hinders the integration of computational modeling with experimental studies. 'clockSim' addresses this gap by providing models and helper functions with step-by-step vignettes. This package opens up system-level exploration of the circadian clock to wet-lab experimentalists, and future development will include additional clock architectures and other gene circuit models. Currently implemented models are based on Leloup and Goldbeter (1998) <doi:10.1177/074873098128999934>.

Last updated

3.18 score 1 stars 4 scripts 86 downloads

gsAnalysis - Miscellaneous tools for genomic sequence analysis

A miscellaneous toolbox for various genomic sequence analysis tasks. Refer to package vignettes for different topics covered in this package. Part of the y3628 analysis suite.

Last updated

cellbiologygenetics

2.00 score 1 scripts

ijAnalysis - Miscellaneous tools for image analysis tasks

A miscellaneous toolbox for various image analysis tasks. Initially contains tools for downstream analysis of my ImageJ plugin Puncta Tracker and hence the ij name. Part of the y3628 analysis suite.

Last updated

2.00 score 1 scripts

Rabe - Adenine base editor analysis

Base editors are emerging molecular sensors for protein-RNA interaction. This package implements a workflow for analysis of adenine base editor datasets. With minimal adjustment it can be used for systematic inquiry of any known single base-pair mutagenesis patterns. Part of the y3628 analysis suite.

Last updated

cellbiologygenetics

2.00 score 1 scripts

y3628 - Base package for the y3628 data analysis suite

Base functionalities used by other packages in the y3628 suite of data analysis tools. These were initially written for various projects during my years at Michigan.

Last updated

cellbiologygenetics

1.78 score 2 dependents