This directory contains the input file for our project, as well as descriptions on how to access certain data that is used for our study but not available here:
- ref_7mers_structure_cpg.xlsx (available)
This is a DNAshapeR reference table generated from one of our other pipelines. Since this data is generated by ourselves, you are more than welcome to use it in anyway you like.
- 41588_2016_BFng3511_MOESM210_ESM.xlsx (freely accessible)
This is supplement table #6 in the Aggarwala and Voight publication. Please see the citation to retrieve this data.
- ben_data_7mer_bayesian_test_training_AFR_10 (by request)
This is the data used by Varun Aggarwala for their paper; it can be downloaded from Dr. Benjamin Voight's Github page, under the git mutvar_fwdRegr-master/raw_data/. Please request access from Dr. Voight before using their data.
- non_coding_all_AFR_before3_after3_folded_all (by request)
This is the data directly generated from Varun's data processing pipeline. It is available in their supplement data, under the directory substitution_rate_paper_code_and_data/noncoding/*.