Last updated: 2020-11-30

Checks: 2 0

Knit directory: rss-net/

This reproducible R Markdown analysis was created with workflowr (version 1.6.2). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

R Markdown file: up-to-date

Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.

Repository version: d6d604e

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.

The results in this page were generated with repository version d6d604e. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated: 


Ignored files:
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    examples/ibd2015_nkcell/ibd2015_Primary_Natural_Killer_cells_from_peripheral_blood_NK_out_66.mat
    Ignored:    examples/ibd2015_nkcell/randinit_results/
    Ignored:    examples/ibd2015_nkcell/results/
    Ignored:    examples/wtccc_bcell/results/

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

These are the previous versions of the repository in which changes were made to the R Markdown (rmd/index.Rmd) and HTML (docs/index.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File Version Author Date Message
html d6d604e xiangzhu 2020-11-30 Build site.
Rmd 5479073 xiangzhu 2020-11-30 wflow_publish(“rmd/index.Rmd”)
html 93ce892 xiangzhu 2020-06-29 Build site.
html 6e21470 Xiang Zhu 2020-06-24 Build site.
Rmd 93089bf Xiang Zhu 2020-06-24 wflow_publish(“rmd/index.Rmd”)
html d0d89cf xiangzhu 2020-03-16 Build site.
Rmd 4f41d06 xiangzhu 2020-03-16 wflow_publish(“rmd/index.Rmd”)
html 41f1c84 xiangzhu 2020-03-15 Build site.
Rmd 7ed83c0 xiangzhu 2020-03-15 wflow_publish(“rmd/index.Rmd”)
html 7d3492e xiangzhu 2020-03-15 Build site.
Rmd 7d5da72 xiangzhu 2020-03-15 wflow_publish(“rmd/index.Rmd”)
html a424171 xiangzhu 2020-03-08 Build site.
Rmd f0aa16b xiangzhu 2020-03-08 wflow_publish("rmd/*.Rmd")
html 6513730 xiangzhu 2020-03-08 Build site.
Rmd a75fdfb xiangzhu 2020-03-08 wflow_publish(“rmd/index.Rmd”)
html 4fc8d7b xiangzhu 2020-03-08 Build site.
Rmd 7d31559 xiangzhu 2020-03-08 wflow_publish(“rmd/index.Rmd”)
html 5c5e8e1 xiangzhu 2020-03-08 Build site.
Rmd c60a5ad xiangzhu 2020-03-08 wflow_publish("rmd/*.Rmd")
html 4ca805b xiangzhu 2020-03-06 Build site.
Rmd 458c7f7 xiangzhu 2020-03-06 wflow_publish(“rmd/index.Rmd”)
html 3f42262 xiangzhu 2020-03-05 Build site.
Rmd aef978c xiangzhu 2020-03-05 wflow_publish(“rmd/index.Rmd”)
html fa3a812 xiangzhu 2020-02-29 Build site.
Rmd ae0293e xiangzhu 2020-02-29 wflow_publish(“rmd/index.Rmd”)
html 822011d xiangzhu 2019-08-24 Build site.
html d610537 xiangzhu 2019-08-24 rename doc folder
html 71b62db xiangzhu 2019-08-24 rename doc folder
html c29572b xiangzhu 2019-08-24 Build site.
Rmd 40ce70d xiangzhu 2019-08-24 wflow_publish(“rmd/index.Rmd”)
html 1cc57e6 xiangzhu 2019-08-24 Build site.
Rmd 167e314 xiangzhu 2019-08-24 wflow_publish(“rmd/index.Rmd”)
html b16c736 xiangzhu 2019-08-24 Build site.
Rmd 040f663 xiangzhu 2019-08-24 wflow_publish(“rmd/index.Rmd”)
Rmd 32e9e0f xiangzhu 2019-08-24 rename rmd folder

Welcome to RSS-NET wiki!

This wiki hosts documentations of RSS-NET software. If you have any question or suggestion about RSS-NET, please feel free to create a new issue and/or send an email to xiangzhu[at]psu.edu.

The RSS-NET methodology and its application to 38 gene regulatory networks and 18 human complex traits are described in the following article:

Xiang Zhu, Zhana Duren, Wing Hung Wong (2020). Modeling regulatory network topology improves genome-wide analyses of complex human traits. bioRxiv. https://doi.org/10.1101/2020.03.13.990010.

All 38 gene regulatory networks used in this study are freely available at suwonglab/rss-net/data.

The full RSS-NET analysis results of 38 networks and 18 traits are freely available at the Results Page

If you find the analysis results, the pre-processed network files, the statistical methods, and/or the open-source software useful for your work, please kindly cite the research article listed above (Zhu et al, 2020).

Installation

This page provides instructions for installing RSS-NET software.

Examples

This page gives the following end-to-end examples of using RSS-NET methods and software.

  1. RSS-NET analysis of two synthetic datasets

  2. RSS-NET analysis of a real-world dataset

These examples are based on simulation studies and data analyses reported in Zhu et al (2020).

Functions

This page outlines functions and scripts associated with RSS-NET methods.

Icons used in this wiki are credited to the Noun Project. This wiki is created using workflowr.