Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data

binned.data | Binned read counts |

binReads | Convert aligned reads from various file formats into read... |

callPeaksMultivariate | Fit a Hidden Markov Model to multiple ChIP-seq samples |

callPeaksReplicates | Fit a multivariate Hidden Markov Model to multiple ChIP-seq... |

callPeaksUnivariate | Fit a Hidden Markov Model to a ChIP-seq sample. |

callPeaksUnivariateAllChr | Fit a Hidden Markov Model to a ChIP-seq sample. |

changeMaxPostCutoff | Adjust sensitivity of peak detection |

changePostCutoff | Change the posterior cutoff of a Hidden Markov Model |

Chromstar | Wrapper function for the 'chromstaR' package |

chromstaR-objects | chromstaR objects |

chromstaR-package | Combinatorial and differential chromatin state analysis for... |

collapseBins | Collapse consecutive bins |

combinatorialStates | Get the (decimal) combinatorial states of a list of... |

combinedMultiHMM | Combined multivariate HMM object |

combineMultivariates | Combine combinatorial states from several Multivariates |

conversion | Conversion of decimal and binary states |

enrichment_analysis | Enrichment analysis |

enrichmentAtAnnotation | Enrichment of (combinatorial) states for genomic annotations |

experiment.table | Experiment data table |

exportFiles | Export genome browser uploadable files |

exportGRangesAsBedFile | Export genome browser viewable files |

fixedWidthBins | Make fixed-width bins |

genes_rn4 | Gene coordinates for rn4 |

genomicFrequencies | Frequencies of combinatorial states |

getCombinations | Get combinations |

getDistinctColors | Get distinct colors |

getStateColors | Get state colors |

heatmapCombinations | Plot a heatmap of combinatorial states |

heatmapCountCorrelation | Read count correlation heatmap |

heatmapTransitionProbs | Heatmap of transition probabilities |

importChromHMMsegmentation | Import ChromHMM segmentation |

loadHmmsFromFiles | Load 'chromstaR' objects from file |

mergeChroms | Merge several 'multiHMM's into one object |

model.combined | Combined multivariate HMM for demonstration purposes |

model.multivariate | Multivariate HMM for demonstration purposes |

model.univariate | Univariate HMM for demonstration purposes |

multiHMM | Multivariate HMM object |

multivariateSegmentation | Multivariate segmentation |

plotExpression | Overlap with expression data |

plotGenomeBrowser | #' Plot a genome browser view #' #' Plot a simple genome... |

plotHistogram | Histogram of binned read counts with fitted mixture... |

plotHistograms | Histograms of binned read counts with fitted mixture... |

plotting | chromstaR plotting functions |

print.combinedMultiHMM | Print combinedMultiHMM object |

print.multiHMM | Print multiHMM object |

print.uniHMM | Print uniHMM object |

readBamFileAsGRanges | Import BAM file into GRanges |

readBedFileAsGRanges | Import BED file into GRanges |

readConfig | Read chromstaR configuration file |

readCustomBedFile | Read bed-file into GRanges |

removeCondition | Remove condition from model |

scanBinsizes | Find the best bin size for a given dataset |

scores | chromstaR scores |

simulateMultivariate | Simulate multivariate data |

simulateReadsFromCounts | Simulate read coordinates |

simulateUnivariate | Simulate univariate data |

state.brewer | Obtain combinatorial states from specification |

stateBrewer | Obtain combinatorial states from experiment table |

subsample | Normalize read counts |

transitionFrequencies | Transition frequencies of combinatorial states |

uniHMM | Univariate HMM object |

unis2pseudomulti | Combine univariate HMMs to a multivariate HMM |

variableWidthBins | Make variable-width bins |

writeConfig | Write chromstaR configuration file |

zinbinom | The Zero-inflated Negative Binomial Distribution |

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