Last updated: 2019-06-26

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Knit directory: HiCiPSC/

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These are the previous versions of the R Markdown and HTML files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view them.

File Version Author Date Message
Rmd a15345d Ittai Eres 2019-06-26 Update index and corresponding figure references to match final version of paper.
html 1ef50e9 Ittai Eres 2019-06-25 Build site.
Rmd 43a213d Ittai Eres 2019-06-25 Update links in analysis.
html 5fda2d6 Ittai Eres 2019-06-25 Build site.
html 2ec8067 Ittai Eres 2019-05-09 Build site.
html db4d599 Ittai Eres 2019-04-24 Build site.
html 6f6db11 Ittai Eres 2019-04-23 Build site.
html a02a602 Ittai Eres 2019-03-14 Build site.
html 972c85a Ittai Eres 2019-03-14 Build site.
Rmd ef02896 Ittai Eres 2019-03-14 Add Linear modeling QC and modify index.Rmd to reflect figures therein
html 158b881 Ittai Eres 2019-03-13 Build site.
Rmd 67d6f15 Ittai Eres 2019-03-13 Update directory storage of files; add in data frame of only contacts fixed within species.
html 3d877d7 Ittai Eres 2019-03-12 Build site.
Rmd 607efb8 Ittai Eres 2019-03-12 Initialize website with index and initial QC file.
Rmd 9945292 Ittai Eres 2019-03-11 Start workflowr project.

This website details computational analyses done for the paper “Reorganization of 3D Genome Structure May Contribute to Gene Regulatory Evolution in Primates”. In this work, I utilized Hi-C and RNA-seq to find 3-dimensional regulatory differences affecting gene expression between humans and chimpanzees. Click on any of the links below to jump to that section of the analysis. Note that, for many interaction analyses, I repeated the same analysis using different normalization and significance-calling schmes (HOMER vs. Juicer); these are the larger headers. Figures 3, 5, and S10 were not created in R and thus are not seen here (I used pyGenomeTracks to make them). All other figures can be found in the associated files, as written below:

Analyses Utilizing Homer

Analyses Utilizing Juicer

TAD Analyses

License

Copyright (c) 2019, Ittai Eres, Kaixuan Luo, Chiaowen Joyce Hsiao, Lauren E. Blake, and Yoav Gilad. All source code and software in this repository are made available under the terms of the GNU GPL v3