As part of the National Library of Medicine Reproducibility Workshop concluded on May 16, 2019, we sought to reproduce the study published by Schmid et. al., 2018 https://doi.org/10.1016/j.celrep.2018.07.104
To simplify software installation and data acquisition we have posted three jupyter notebooks:
- InstallNeededPrograms_30157438.ipynb
- DownloadNeededData_30157438.ipynb
- InstallGenomeAssemblies.ipynb
We have begun converting the rmd files documented in https://github.com/manschmi/MexNab_3seq to jupyter notebooks that could be followed line by line:
- 1_QC_and_mapping.ipynb
- 2_GenomicA_masking.ipynb
- 3_Sp_normalization.ipynb
This is in no way a completed endeavor, however we commend Schmid et al., in their documentation and feel confident that given sufficient time we would have been successful in reproducing their data analysis pipeline.