Files in cemordaunt/comethyl
An R Package for Weighted Region Comethylation Network Analysis

.Rbuildignore

DESCRIPTION

LICENSE

NAMESPACE

Paper/Comethyl Module Replication.R Paper/comethyl CpG Clusters.R Paper/comethyl Gene Body.R R/Analyze_Module_Preservation.R R/Annotate_Modules.R R/Build_Comethylation_Network.R R/Examine_Region_Methylation.R R/Explore_Module_Trait_Correlations.R R/Get_and_Filter_CpGs.R R/Get_and_Filter_Regions.R R/Investigate_Functional_Enrichments.R R/Visualize_Comethylation_Network.R R/comethyl.R README.md

_pkgdown.yml

docs/404.html

docs/LICENSE-text.html

docs/LICENSE.html

docs/articles/CpG Cluster Analysis/CpG_Totals.png

docs/articles/CpG Cluster Analysis/Filtered_Region_Plots.png

docs/articles/CpG Cluster Analysis/ME_Trait_Correlation_Heatmap.png

docs/articles/CpG Cluster Analysis/Module_Correlation_Heatmap.png

docs/articles/CpG Cluster Analysis/Module_ME_Dendrogram.png

docs/articles/CpG Cluster Analysis/Region_Dendrograms.png

docs/articles/CpG Cluster Analysis/Region_Totals.png

docs/articles/CpG Cluster Analysis/Sample_Correlation_Heatmap.png

docs/articles/CpG Cluster Analysis/Sample_Dendrogram.png

docs/articles/CpG Cluster Analysis/Sample_ME_Dendrogram.png

docs/articles/CpG Cluster Analysis/Sample_ME_Heatmap.png

docs/articles/CpG Cluster Analysis/Sig_ME_Trait_Correlation_Heatmap.png

docs/articles/CpG Cluster Analysis/Soft_Power_Plots.png

docs/articles/CpG Cluster Analysis/Top_ME_Trait_Correlation_Heatmap.png

docs/articles/CpG Cluster Analysis/Trait_Dendrogram.png

docs/articles/CpG Cluster Analysis/Unfiltered_Region_Plots.png

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docs/articles/CpG Cluster Analysis/bisque4_ME_Diagnosis_Dotplot.png

docs/articles/CpG Cluster Analysis/bisque4_Module_Enrichment_Plot.png

docs/articles/CpG Cluster Analysis/bisque4_Module_Methylation_Diagnosis_Heatmap.png

docs/articles/CpG Cluster Analysis/paleturquoise_ME_Bcells_Scatterplot.png

docs/articles/CpG Cluster Analysis/paleturquoise_ME_Granulocytes_Scatterplot.png

docs/articles/CpG Cluster Analysis/paleturquoise_Module_Enrichment_Plot.png

docs/articles/CpG Cluster Analysis/paleturquoise_Module_Methylation_Bcells_Heatmap.png

docs/articles/CpG Cluster Analysis/paleturquoise_Module_Methylation_Granulocytes_Heatmap.png

docs/articles/CpG_Cluster_Analysis.html

docs/articles/CpG_Cluster_Analysis_files/header-attrs-2.9/header-attrs.js

docs/articles/Gene Body Analysis/Filtered_Region_Plots.png

docs/articles/Gene Body Analysis/ME_Trait_Correlation_Heatmap.png

docs/articles/Gene Body Analysis/Module_Correlation_Heatmap.png

docs/articles/Gene Body Analysis/Module_ME_Dendrogram.png

docs/articles/Gene Body Analysis/Region_Dendrograms.png

docs/articles/Gene Body Analysis/Region_Totals.png

docs/articles/Gene Body Analysis/Sample_Correlation_Heatmap.png

docs/articles/Gene Body Analysis/Sample_Dendrogram.png

docs/articles/Gene Body Analysis/Sample_ME_Dendrogram.png

docs/articles/Gene Body Analysis/Sample_ME_Heatmap.png

docs/articles/Gene Body Analysis/Sig_ME_Trait_Correlation_Heatmap.png

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docs/articles/Gene Body Analysis/Top_ME_Trait_Correlation_Heatmap.png

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docs/articles/Gene Body Analysis/greenyellow_ME_Granulocytes_Scatterplot.png

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docs/articles/Gene Body Analysis/greenyellow_Module_Enrichment_Plot.png

docs/articles/Gene Body Analysis/greenyellow_Module_Methylation_Granulocytes_Heatmap.png

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docs/articles/Gene_Body_Analysis.html

docs/articles/Gene_Body_Analysis_files/header-attrs-2.9/header-attrs.js

docs/articles/Introduction.html

docs/articles/Module Preservation/Filtered_Region_Plots.png

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docs/articles/comethyl.html

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exec/Comethyl_Analysis_Pipeline.R man/adjustRegionMeth.Rd man/annotateModule.Rd man/comethyl.Rd man/enrichModule.Rd

man/figures/comethyl.png

man/filterCpGs.Rd man/filterRegions.Rd man/getCor.Rd man/getCpGs.Rd man/getCpGtotals.Rd man/getDendro.Rd man/getGeneList.Rd man/getMEtraitCor.Rd man/getModuleBED.Rd man/getModulePreservation.Rd man/getModules.Rd man/getPCs.Rd man/getRegionMeth.Rd man/getRegionTotals.Rd man/getRegions.Rd man/getSoftPower.Rd man/listOntologies.Rd man/plotCpGtotals.Rd man/plotDendro.Rd man/plotEnrichment.Rd man/plotHeatmap.Rd man/plotMEtraitCor.Rd man/plotMEtraitDot.Rd man/plotMEtraitScatter.Rd man/plotMethTrait.Rd man/plotModulePreservation.Rd man/plotRegionDendro.Rd man/plotRegionStats.Rd man/plotRegionTotals.Rd man/plotSDstats.Rd man/plotSoftPower.Rd

vignettes/CpG Cluster Analysis/CpG_Totals.png

vignettes/CpG Cluster Analysis/Filtered_Region_Plots.png

vignettes/CpG Cluster Analysis/Filtered_SD_Plots.png

vignettes/CpG Cluster Analysis/ME_Trait_Correlation_Heatmap.png

vignettes/CpG Cluster Analysis/Module_Correlation_Heatmap.png

vignettes/CpG Cluster Analysis/Module_ME_Dendrogram.png

vignettes/CpG Cluster Analysis/Region_Dendrograms.png

vignettes/CpG Cluster Analysis/Region_Totals.png

vignettes/CpG Cluster Analysis/Sample_Correlation_Heatmap.png

vignettes/CpG Cluster Analysis/Sample_Dendrogram.png

vignettes/CpG Cluster Analysis/Sample_ME_Dendrogram.png

vignettes/CpG Cluster Analysis/Sample_ME_Heatmap.png

vignettes/CpG Cluster Analysis/Soft_Power_Plots.png

vignettes/CpG Cluster Analysis/Trait_Dendrogram.png

vignettes/CpG Cluster Analysis/Unfiltered_Region_Plots.png

vignettes/CpG Cluster Analysis/Unfiltered_SD_Plots.png

vignettes/CpG Cluster Analysis/bisque4_ME_Diagnosis_Dotplot.png

vignettes/CpG Cluster Analysis/bisque4_Module_Enrichment_Plot.png

vignettes/CpG Cluster Analysis/bisque4_Module_Methylation_Diagnosis_Heatmap.png

vignettes/CpG Cluster Analysis/paleturquoise_ME_Bcells_Scatterplot.png

vignettes/CpG Cluster Analysis/paleturquoise_ME_Granulocytes_Scatterplot.png

vignettes/CpG Cluster Analysis/paleturquoise_Module_Enrichment_Plot.png

vignettes/CpG Cluster Analysis/paleturquoise_Module_Methylation_Bcells_Heatmap.png

vignettes/CpG Cluster Analysis/paleturquoise_Module_Methylation_Granulocytes_Heatmap.png

vignettes/CpG_Cluster_Analysis.Rmd

vignettes/Gene Body Analysis/Filtered_Region_Plots.png

vignettes/Gene Body Analysis/Filtered_SD_Plots.png

vignettes/Gene Body Analysis/ME_Trait_Correlation_Heatmap.png

vignettes/Gene Body Analysis/Module_Correlation_Heatmap.png

vignettes/Gene Body Analysis/Module_ME_Dendrogram.png

vignettes/Gene Body Analysis/Region_Dendrograms.png

vignettes/Gene Body Analysis/Region_Totals.png

vignettes/Gene Body Analysis/Sample_Correlation_Heatmap.png

vignettes/Gene Body Analysis/Sample_Dendrogram.png

vignettes/Gene Body Analysis/Sample_ME_Dendrogram.png

vignettes/Gene Body Analysis/Sample_ME_Heatmap.png

vignettes/Gene Body Analysis/Soft_Power_Plots.png

vignettes/Gene Body Analysis/Trait_Dendrogram.png

vignettes/Gene Body Analysis/Unfiltered_Region_Plots.png

vignettes/Gene Body Analysis/Unfiltered_SD_Plots.png

vignettes/Gene Body Analysis/Unfiltered_SD_Plots_Zoom.png

vignettes/Gene Body Analysis/greenyellow_ME_CD4T_Scatterplot.png

vignettes/Gene Body Analysis/greenyellow_ME_CD8T_Scatterplot.png

vignettes/Gene Body Analysis/greenyellow_ME_Granulocytes_Scatterplot.png

vignettes/Gene Body Analysis/greenyellow_ME_Home_Ownership_Dotplot.png

vignettes/Gene Body Analysis/greenyellow_Module_Enrichment_Plot.png

vignettes/Gene Body Analysis/greenyellow_Module_Methylation_CD4T_Heatmap.png

vignettes/Gene Body Analysis/greenyellow_Module_Methylation_CD8T_Heatmap.png

vignettes/Gene Body Analysis/greenyellow_Module_Methylation_Granulocytes_Heatmap.png

vignettes/Gene_Body_Analysis.Rmd

vignettes/Module Preservation/Filtered_Region_Plots.png

vignettes/Module Preservation/Module_Preservation_Statistics_Plot.png

vignettes/Module Preservation/Region_Totals.png

vignettes/Module Preservation/Sample_Dendrogram.png

vignettes/Module Preservation/Soft_Power_Plots.png

vignettes/Module Preservation/Unfiltered_Region_Plots.png

vignettes/Module Preservation/Unfiltered_SD_Plots.png

vignettes/Module_Preservation.Rmd vignettes/comethyl.Rmd

cemordaunt/comethyl documentation built on Oct. 20, 2023, 5:47 p.m.

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cemordaunt/comethyl
An R Package for Weighted Region Comethylation Network Analysis

Files in cemordaunt/comethyl
An R Package for Weighted Region Comethylation Network Analysis

R Package Documentation

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cemordaunt/comethyl An R Package for Weighted Region Comethylation Network Analysis

Files in cemordaunt/comethyl An R Package for Weighted Region Comethylation Network Analysis

R Package Documentation

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We want your feedback!

cemordaunt/comethyl
An R Package for Weighted Region Comethylation Network Analysis

Files in cemordaunt/comethyl
An R Package for Weighted Region Comethylation Network Analysis