This repository contains the information and scripts for analysis in Shim et al. (2021) and their results.
- The main manuscript and supplementary material
- the multiseq R package and its vignette.
- ATAC-seq data (hdf5 format) for nine samples can be downloaded from this link. These files have been converted from bam files using a script in multiseq_Shim_et_al/scripts/bamTOhdf5.md.
- ATAC-seq analysis
- Information on the 242,714 regions included in the analysis (the top 5% of regions with the highest chromatin accessibility) and results from the analysis are in multiseq_Shim_et_al/ATACseq/information_results.
- A script to for each region 1) extract ATAC-seq count data at the region on 6 samples (6 by 1024) from the hdf5 files and 2) do data-preprocessing as described in Shim et al (2021) is in multiseq_Shim_et_al/scripts/ATAC-seq.Rmd.
- Once we have the count data after the data-preprocessing, we can follow the vignette of the multiseq R package to 1) run multiseq, and 2) plot estimated effect sizes as shown in Shim et al (2021).
- Simulation procedure described in Shim et al (2021) has been implemented in the function
sample.from.Binomial.with.Overdispersionof the multiseq R package. See the vignette of the multiseq R package to see how to use this function.
Copyright (c) 2021-2023, Heejung Shim
All source code and software in this repository is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version. See the LICENSE file for the full text of the license.