# Predicting functional networks and modules of chromatin factors controlling adult stem cell fate from RNA interference screens

## Documentation for package ‘Mulder2012’ version 0.2.5

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

Arora2010 | Raw and processed data for the application of PANs to Ewing's sarcoma
Arora2010.BMfitting | Fitting a beta-mixture model to association scores
Arora2010.fig | A pipeline function to reproduce the main figures of network analyses in Wang et al 2012 for Arora S et al 2010
Arora2010.hypergeo | Hypergeometric tests for pathway analysis
Arora2010.InferPAN | Infer a posterior association network given a fitted BetaMixture object
Arora2010.module.visualize | Infer a posterior association network given a fitted BetaMixture object
Arora2010.ModuleSearchByPvclust | Searching for enriched functional modules by pvclust
Arora2010.pathway | Raw and processed data for the application of PANs to Ewing's sarcoma
Arora2010.pipeline | A pipeline to do network analyses in Wang et al 2012 for Arora S et al 2010
bm_Arora2010 | Raw and processed data for the application of PANs to Ewing's sarcoma
bm_ext_Mulder2012 | Raw and processed data for the application to epidermal stem cells
bm_Mulder2012 | Raw and processed data for the application to epidermal stem cells
dist.pvclust4PAN | Compute distances between gene phenotypes for pvclust
GSEARandomWalkFig | Plot a figure illustrating enrichment analysis results
Mulder2012 | Raw and processed data for the application to epidermal stem cells
Mulder2012.BMfitting | Fitting a beta-mixture model to association scores
Mulder2012.BMfitting.extended | Fitting a beta-mixture model to association scores
Mulder2012.fig | A pipeline function to reproduce the main figures of network analyses in Mulder K et al 2012 and Wang et al 2012
Mulder2012.InferPAN | Infer a posterior association network given a fitted BetaMixture object
Mulder2012.module.visualize | Infer a posterior association network given a fitted BetaMixture object
Mulder2012.ModuleSearchByPvclust | Searching for enriched functional modules by pvclust
Mulder2012.PINdbProteins | Raw and processed data for the application to epidermal stem cells
Mulder2012.pipeline | A pipeline to do network analyses for Mulder 2012
Mulder2012.PPI | Raw and processed data for the application to epidermal stem cells
Mulder2012.PPIEnrich | Raw and processed data for the application to epidermal stem cells
Mulder2012.PPIenrich | Enrichment analyses of posterior probabilities in protein-protein interactions
Mulder2012.PPIPre | Extracting protein-protein interactions from PINdb
Mulder2012.rawScreenAnnotation | Raw and processed data for the application to epidermal stem cells
Mulder2012.rawScreenData | Raw and processed data for the application to epidermal stem cells
Mulder2012.RNAiPre | Preprocessing of the raw RNAi screens
pan_Arora2010 | Raw and processed data for the application of PANs to Ewing's sarcoma
pan_ext_Mulder2012 | Raw and processed data for the application to epidermal stem cells
pan_Mulder2012 | Raw and processed data for the application to epidermal stem cells
parPvclust4PAN | Compute distances between gene phenotypes for pvclust
PINdbProteins | Raw and processed data for the application to epidermal stem cells
PPI | Raw and processed data for the application to epidermal stem cells
PPIEnrich_Mulder2012 | Raw and processed data for the application to epidermal stem cells
proteinModules | Raw and processed data for the application to epidermal stem cells
pw.rslt | Raw and processed data for the application of PANs to Ewing's sarcoma
rawScreenAnnotation | Raw and processed data for the application to epidermal stem cells
rawScreenData | Raw and processed data for the application to epidermal stem cells