R Investigation of ChIP-chip Oligoarrays

arrayImage | Function to visualize spatial distribution of raw intensities |

asExprSet | converts a Ringo MAList into an ExpressionSet |

autocorr | Function to compute auto-correlation of probe intensities |

cherByThreshold | Function to identify chers based on thresholds |

cherClass | Class "cher" - ChIP-enriched region |

chipAlongChrom | Visualize ChIP intensities along the chromosome |

chipAlongChromOld | Visualize ChIP intensities along the chromosome |

compute_gc | Compute the GC content of DNA and probe sequences |

computeRunningMedians | Function to compute running medians on a tiling expression... |

compute_sliding_t | Function to compute sliding T statistics on a tiling... |

corrPlot | Function to plot correlation of different samples |

exportCherList | Function to export cherList into a file |

extractProbeAnno | Build probeAnno from match positions in an RGList |

features2Probes | Function for mapping genomic features to probes |

findChersOnSmoothed | Find ChIP-enriched regions on smoothed ExpressionSet |

ftr2xys | Convert a NimbleScan ftr-file into a xys-file |

getFeats | Utility function to extract all features from a cherList |

newCER | Create a list object of class cher |

nimblegenNorm | Function to compute scaled log-ratios |

nonzero | Methods for Function nonzero |

plotAutocorr | Plots auto-correlation of probe intensities |

plotBM | Visualization of a binary matrix |

plot_cher | Plot identified Chers |

posToProbeAnnoEnvironment | Function for creating a probeAnno environment |

preprocess | Preprocess Raw ChIP-chip Intensities |

probeAnnoClass | Class "probeAnno" |

qopS4 | Class "qop" Quantiles Over Positions |

quantilesOverPositions | show ChIP-chip data aligned over genome features, e.g. TSSs |

readNimblegen | Function to read in Nimblegen Intensity Text Files |

regionoverlap | Function to compute overlap of genomic regions |

relateCERs | Relate found Chers to genomic features |

Ringo-internal | Internal Ringo functions |

sigGOTable | Obtain significant GO terms for a list of genes |

sliding_meansd | Compute mean and standard deviation of scores in a sliding... |

sliding_quantile | Compute quantile of scores in a sliding window |

twoGaussiansNull | Estimate a threshold from Gaussian mixture distribution |

upperBoundNull | function to estimate upper limit of null distribution |

validProbeAnno | Function to check a probeAnno environment |

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