Man pages for ttriche/chromophobe
Explore genomic state models, predictions, sample compositions & overlaps
| addRoadmapColors | convenience function to relabel states with standard colors |
| aggregateStates | merge segments that are all in a row, but avoid slopping... |
| asRaggedExperiment | Take a set of segmentations and make them into a... |
| chromophobe-package | Package to explore genomic enrichments for ChromHMM and... |
| collapseAt | Collapse a SummarizedExperiment-like object over a GRanges,... |
| colorHMM | add (new) colors to a ChromHMM track |
| compressAndExportHMM | Reduce a (usually simplified) segmentation, export to BED,... |
| donutPlot | simple function for a donut plot of state width/count... |
| genomeFrac | convenience function for generating donut plots of basepair... |
| GenomicSegmentation | A subclass of GRanges with a trackLine slot, similar to... |
| GenomicSegmentationList | Like GRangesList, but with a trackLine slot, similar to... |
| getConditions | list all the conditions found in a BED file of a stacked HMM |
| getStackedState | pull out ranges from a stacked HMM that differ by condition... |
| getState | pull out ranges from a GenomicSegmentation or similar |
| getStates | list all the states found in a BED file of an HMM, stacked or... |
| importAndSimplifyHMM | import and simplify a REMC or ENCODE ChromHMM track |
| makeAndExportDisjointHMM | convenience function to disjoin and dump a set of HMMs |
| makeAndExportStackedHMM | convenience function for dumping sets of chromHMM "contrasts"... |
| regionFrac | convenience function for generating donut plots of count... |
| simplifyHMM | convenience function for adding simplified names & colors to... |
| stackedPlot | simple function for a circular barchart of state transitions... |
| stackHMMs | build a poor man's stacked HMM |
