Analysis of Genome Segmentations by segmenTier

add_alphas | replace alpha values of an RGB string color vector |

alignData | align genome data at specified coordinates (e.g. TSS) |

annotateTarget | annotate target segments by overlapping query segments |

ash | asinh data transformation |

calculatePhase | calculate peak phase |

ci95 | calculate 95 data vector using a t-distribution |

circ.dens | circular density |

clusterAnnotation | clustering enrichment scan |

clusterAverages | calculates cluster averages |

clusterCluster | calculates overlaps between two clusterings |

clusterColors | get color vector for clustered features |

clusterTimeseries2 | Cluster a processed time-series with k-means or flowClust |

collectOvlStats | Collect statistics from from 'segmentOverlap' |

complex2degree | convert complex numbers to degrees |

coor2index | convert chromosome coordinates to continuous index |

dense2d | 2D density heatmap plot |

expandCircularFeatures | Splits genome features spanning annotated ends of circular... |

fillGenome | Get inter-segments |

findAACodon | find genomic coordinates of amino acid position in a protein... |

getChrSum | Generate chromosome index 'chrS' from lengths |

get_fft | Discrete Fourier Transformation |

getOverlapStats | Statistics of overlaps between two segment sets. |

getSegmentClasses | splits segmenTier segment class strings into classes |

getSegmentClassTable | splits segmenTier classes into a table |

gff2tab | parse a GFF3 file into a table |

idx2chr | get the chromosome from continuous index |

idx2coor | Simple version of 'index2coor' for single values |

idx2str | get the strand from continuous index |

image_matrix | wrapper for 'image' plotting a data matrix in the orientation... |

index2coor | convert continuous index to chromosome coordinates (reverse... |

insertRows | insert rows as specified positions |

lg2r | log2 ratio normalization |

log_1 | log trafo handling zeros by adding 1 |

ma | moving average using 'filter' |

meanzero | mean-0 normalization |

mergeCluster | using 'flowMerge' to merge clusterings |

parseAnnotation | parse an annotation file (a bidirectional map) |

parseGEOSoft | parse GO Soft archives |

phaseDist | Calculates phase distributions |

plotBIC | plot BIC from flowclusterTimeseries |

plot_cdfLst | plot multiple cumulative distribution functions |

plot.clusteraverages | plots cluster averages |

plotClusterLegend | plot sorted clustering as color table |

plotClusters | plots cluster averages |

plotdev | Switch between plot devices |

plotDFT | plot polar coordinates |

plotOverlaps | plot cluster-cluster or segment-segment overlaps |

plotSingles | plot indivividual time series in cluster context |

presegment | Pre-segmentation of the time-series |

pvalDist | cluster p-value summary |

randomSegments | randomize locations of input segments |

range2nt | calculates letter frequences in ranges of strings |

readDist | distribution of read-counts, i.e., the mean, var, min&max and... |

reCluster | re-cluster clustering by 'kmeans' |

relabelClusters | relabels cluster labels by their sorting |

removeCircularFeatures | NOT WORKING - Undo 'expandCircularFeatures' searches for... |

revcomp | calculate reverse complement of RNA or DNA |

segmentAverage | Average read-counts of segments |

segmentJaccard | Jaccard-Index overlap test for classes of segments (genomic... |

segmenTools | segmenTools : analysis of genome segmentations by segmenTier |

segmentOverlap | Overlaps between two sets of chromosome segments |

selected | get clustering ID |

seq2nt | calculate local nucleotide content |

sortOverlaps | sorts cluster overlap structure by p-values |

splitsegs | splits segments that span chromosome ends |

summarizeGEOSoft | summarize GEOSoft probes |

switchStrand | switches the strand information (reverse<->forward) of... |

tab2gff | creates a gff3-like table |

tagDuplicates | Tag duplicate names by increasing numbers. |

testPhase | tests phase recovery by 'calculatePhase' |

whichSegment | which segment covers a position |

writeSegments | write out segment data to individual files |

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