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


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Documentation for package ‘Mulder2012’ version 0.2.3

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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