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Epigenomics-Screw / Screw

SCREW: A Reproducible Workflow for Single-Cell Epigenomics
MIT License
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Create a complete workflow for the analysis of the Smallwood 2014 data #34

Open oneillkza opened 6 years ago

oneillkza commented 6 years ago

Description

As a bioinformatician, I would like to run the complete workflow, including generating QC plots, pairwise clustering, regional methylation, and DMR analysis on the Smallwood 2014 data set, in order to include it in the broader meta-analysis.

Estimate

5

Priority

SHOULD

Notes

Should be based on #30, depends on #33

https://www.nature.com/nmeth/journal/v11/n8/full/nmeth.3035.html https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1370522

oneillkza commented 6 years ago

Repo: https://github.com/Epigenomics-Screw/Smallwood_2014_example

oneillkza commented 6 years ago

@jjonphl and @klimstef, while we're getting the base pipeline tidied up and ready for you to run on these data sets, something which you could do would be to write up the README.md for each of these, and potentially expand the Farlik_2016_example README as well.

oneillkza commented 6 years ago

(ie add links to the data, the paper, and a brief description)

jjonphl commented 6 years ago

@oneillkza and @klimstef, sorry I am no help writing up anything that is not code related. My biology is pedestrian-level and I have no (organic?) chemistry skills to speak of.