Man pages for ben-laufer/DMRichR
Enrich your DMR Analysis with the Tidyverse
| annotateRegions | Annotate DMRs and blocks |
| annotationDatabases | Load annotation databases |
| arrayLift | LiftOver Infinium array probe IDs to hg38 coordinates |
| CGi | Extract methylation values from CpG islands |
| chromHMM | Chromatin state enrichments |
| chromHMM_heatmap | Chromatin state heatmap |
| CpGs | Extract single CpG methylation values |
| densityPlot | Density plot of extracted methylation values |
| DMparseR | Combined plot of stratified gene region and CpG annotation... |
| DM.R | Run the pipeline |
| DMReport | Create an html report of DMRs or blocks |
| DMRichCpG | CpG annotation enrichment testing |
| DMRichGenic | Gene region enrichment testing |
| DMRichPlot | Plot gene region and CpG annotation enrichment testing |
| DMRichR | DMRichR |
| dmrList | Stratify DMRs by directionality |
| dot-onAttach | onAttach |
| extend | Extend genomic ranges |
| getBackground | bsseq style background regions |
| getCpGs | Obtain CpG island, CpG shore, CpG shelf, and open sea... |
| getExons | Obtain exons for plotting |
| gg_color_hue | ggplot2 colors |
| globalStats | Test for global methylation differences |
| GOfuncR | GOfuncR gene ontology enrichment testing |
| GOplot | Plot slimmed GO results |
| gr2bed | Save a genomic ranges object as a bed file |
| HOMER | Transcription factor motif analysis |
| imprintOverlap | Imprinted gene enrichment testing |
| Manhattan | Manhattan plot |
| methylLearn | Machine learning feature selection |
| PCA | PCA plot of extracted methylation values |
| pipe | Pipe operator |
| plotDMRs2 | Plot Differentially Methylated Regions |
| prepareHOMER | Save regions for HOMER |
| processBismark | Preprocess cytosine reports |
| read_excel_all | Read entire excel document |
| roadmap | Chromatin mark enrichments |
| roadmap_heatmap | Chromatin mark heatmap |
| slimGO | Slim GO results |
| smooth2txt | Save regions and methylation values |
| smoothPheatmap | DMR heatmap |
| windows | Extract methylation values from tiled genomic windows |
