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CHIPLEY.DEV - Always improving my interactive pipeline for ChIPseq.

Currently only compatible with a server that uses Slurm job scheduling.

Contact Kenneth Lim, [email protected] with questions.

I. GENERAL

Ripley was originally designed to string together a series of scripts that analyze RNA-seq data in order to analyze them as efficiently as possible with as little user interaction as possible. It kept records of the various parameters and commands that were executed. Ripley.Pro took the idea of Ripley and added features for simpler usage and more flexibility. Ripley.Pro has templates for adding new scripts and tools to the pipeline, so the user can mix and match their analysis tools, as well as a simple progress report and resubmission feature in the interface, which allows users to check on the progress of their data analysis without having to search through subdirectories.

The user is responsible for 2 things: 1) Creating a 'task sheet', which contains some metadata for your current dataset as well as parameters to some of the necessary functions in the pipeline. A single task sheet represents a single dataset.

II. WORKFLOW

III. VARIABLE INDEX