Summary, annotation and visualization of genomic data

annotateWithFeatureFlank-methods | Function to annotate a given GRanges object with... |

annotateWithFeature-methods | Function to annotate given GRanges object with a given... |

annotateWithFeatures-methods | Annotate given ranges with genomic features |

annotateWithGeneParts-methods | Annotate given object with promoter, exon, intron and... |

annotatGrWithGeneParts | annotatGrWithGeneParts function |

AnnotationByFeature-class | An S4 class that information on overlap of target features... |

AnnotationByGeneParts-class | An S4 class that information on overlap of target features... |

AnnotationByGeneParts-methods | Get distance to nearest TSS and gene id from... |

bed12ToExons | bed12ToExons function |

bed12ToIntrons | bed12ToIntrons function |

binMatrix-methods | Bins the columns of a matrix using a user provided function |

binMax | Function that computes a maximum value for each bin |

binMean | Function that computes a mean value for each bin |

binMedian | Function that computes a median value for each bin |

binMin | Function that computes a minimum value for each bin |

binner | binner function |

binSum | Function that computes a sum of values in a bin |

cage | Example CAGE data set. |

calculateOverlapSignificance-methods | function that calculates the significance of overlaps of two... |

checkBedValidity | checkBedValidity function |

checkClass | checkClass function |

compressedAndUrl2temp | compressedAndUrl2temp function |

constrainRanges | constrainRanges function |

convertBed2Exons-methods | convert a data frame read-in from a bed file to a GRanges... |

convertBed2Introns-methods | convert a data frame read-in from a bed file to a GRanges... |

convertBedDf-methods | convert a data frame read-in from a bed file to a GRanges... |

cpgi | Example CpG island data set. |

c.ScoreMatrix | c.ScoreMatrix |

c.ScoreMatrixList | c.ScoreMatrixList |

detectUCSCheader | detectUCSCheader function |

distance2NearestFeature | distance2NearestFeature function |

enrichmentMatrix-ScoreMatrixList-method | Compute an enrichment of IP over control both stored in... |

enrichmentMatrix-ScoreMatrixList-ScoreMatrix-method | Compute an enrichment of IP (stored in ScoreMatrixList... |

enrichmentMatrix-ScoreMatrix-method | Compute an enrichment of IP over control both stored in... |

file.ext | file.ext function |

findFeatureComb-methods | Find combitations of genomic features |

galpTo2Ranges | galpTo2Ranges function |

genes | Example RefSeq genes data set. |

getColors | getColors function |

getFeatsWithTargetsStats-methods | Get the percentage/count of annotation features overlapping... |

getFlanks-methods | Function to get upstream and downstream adjecent regions to a... |

getMembers-methods | Get the membership slot of AnnotationByFeature |

getRandomEnrichment-methods | get enrichment based on randomized feature overlap |

getTargetAnnotationStats-methods | Get the percentage of target features overlapping with... |

gffToGRanges | Converts a gff formated data.frame into a GenomicRanges... |

heatMatrix | Draw a heatmap of a given ScoreMatrix object |

heatMeta | Heatmap for meta-region profiles |

heatTargetAnnotation-methods | Plots the percentage of overlapping intervals with genomic... |

intersectScoreMatrixList-methods | Get common rows from all matrices in a ScoreMatrixList object |

listSliceMax | Function creates a matrix storing data with desirable number... |

listSliceMean | Function creates a matrix storing data with desirable number... |

listSliceMedian | Function creates a matrix storing data with desirable number... |

listSliceMin | Function creates a matrix storing data with desirable number... |

listSliceSum | Function creates a matrix storing data with desirable number... |

Max_c | Function that computes a max value |

Mean_c | Function that computes a mean value |

Median_c | Function that computes a median value |

Min_c | Function that computes a min value |

multiHeatMatrix | Draw multiple heatmaps from a ScoreMatrixList object |

Ops-numeric-ScoreMatrixList-method | Ops method for a ScoreMatrixList object. It enables to use... |

Ops-ScoreMatrixList-numeric-method | Ops method for a ScoreMatrixList object. It enables to use... |

Ops-ScoreMatrixList-ScoreMatrixList-method | Ops method for a ScoreMatrixList object. It enables to use... |

Ops-ScoreMatrix-ScoreMatrix-method | Ops method for a ScoreMatrix object. It enables to use... |

orderBy-methods | Reorder all elements of a ScoreMatrixList to a given ordering... |

patternMatrix-methods | Get scores that correspond to k-mer or PWM matrix occurrence... |

plotMeta | Line plot(s) for meta-region profiles |

plotTargetAnnotation-methods | Plot annotation categories from AnnotationByGeneParts or... |

promoters | Example promoter data set. |

RandomEnrichment-class | An S4 class for storing 'getRandomEnrichment' function... |

randomizeFeature-methods | function that randomizes the genomic coordinates |

readBam | readBam function |

readBed | Read a BED file and convert it to GRanges. |

readBigWig | readBigWig function |

readBroadPeak | A function to read the Encode formatted broad peak file into... |

readFeatureFlank-methods | A function to read-in genomic features and their upstream and... |

readGeneric | Read a tabular file and convert it to GRanges. |

readNarrowPeak | A function to read the Encode formatted narrowPeak file into... |

readTableFast | readTableFast function |

readTranscriptFeatures-methods | Function for reading exon intron and promoter structure from... |

read.zip | read.zip function |

scaleScoreMatrixList | Scale the ScoreMatrixList |

scaleScoreMatrix-methods | Scales the values in the matrix by rows and/or columns |

ScoreMatrixBin-methods | Get bin score for bins on each window |

ScoreMatrix-class | An S4 class for storing 'ScoreMatrix' function results |

ScoreMatrixList-class | An S4 class for storing a set of 'ScoreMatrixList' |

ScoreMatrixList-methods | Make ScoreMatrixList from multiple targets |

ScoreMatrix-methods | Get base-pair score for bases in each window |

show-methods | show method for some of the genomation classes |

sub-ScoreMatrix-ANY-ANY-ANY-method | Extract method for a ScoreMatrix object. |

sub-ScoreMatrixList-ANY-ANY-ANY-method | Extract method for a ScoreMatrixList object. |

Sum_c | Function that computes a sum value |

target.type | target.type function |

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.