https://github.com/drisso/peixoto2015_tutorial
Tutorial to reproduce the analysis of Peixoto et al. (2015)
https://github.com/drisso/peixoto2015_tutorial
Last synced: over 1 year ago
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Tutorial to reproduce the analysis of Peixoto et al. (2015)
- Host: GitHub
- URL: https://github.com/drisso/peixoto2015_tutorial
- Owner: drisso
- Created: 2015-06-01T22:13:21.000Z (about 11 years ago)
- Default Branch: master
- Last Pushed: 2015-11-25T19:09:38.000Z (over 10 years ago)
- Last Synced: 2025-01-09T14:13:02.973Z (over 1 year ago)
- Language: HTML
- Size: 25.7 MB
- Stars: 9
- Watchers: 3
- Forks: 11
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
## Tutorial to reproduce the analysis of [Peixoto et al. (2015)](https://nar.oxfordjournals.org/content/43/16/7664.full)
### Analysis of FC and OLM datasets
All the needed input files are in the [Peixoto_Input_for_Additional_file_1](Peixoto_Input_for_Additional_file_1) directory.
This tutorial has been tested with R 3.2.0.
[Peixoto_Additional_File_1.Rmd](Peixoto_Additional_File_1.Rmd) contains the Rmarkdown and can be run to reproduce the full report.
[Peixoto_Additional_File_1.R](Peixoto_Additional_File_1.R) contains a pure R script and can be sourced to any R session.
[Peixoto_Additional_File_1.html](Peixoto_Additional_File_1.html) and [Peixoto_Additional_File_1.pdf](Peixoto_Additional_File_1.pdf) contain the results of the analysis. Please refer to the Section "Session Info" for details on the package versions used.
### Analysis of publicly available data
The processed expression data from GEO are available in the [Peixoto_Input_for_Additional_file_2](Peixoto_Input_for_Additional_file_2) directory.
[Peixoto_Additional_File_2.Rmd](Peixoto_Additional_File_2.Rmd) contains the Rmarkdown and can be run to reproduce the analysis.
[Peixoto_Additional_File_2.html](Peixoto_Additional_File_2.html) contains the results.