genomation: Summary, annotation and visualization of genomic data

A package for summary and annotation of genomic intervals. Users can visualize and quantify genomic intervals over pre-defined functional regions, such as promoters, exons, introns, etc. The genomic intervals represent regions with a defined chromosome position, which may be associated with a score, such as aligned reads from HT-seq experiments, TF binding sites, methylation scores, etc. The package can use any tabular genomic feature data as long as it has minimal information on the locations of genomic intervals. In addition, It can use BAM or BigWig files as input.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("genomation")
AuthorAltuna Akalin [aut, cre], Vedran Franke [aut, cre], Katarzyna Wreczycka [aut], Alexander Gosdschan [ctb], Liz Ing-Simmons [ctb]
Bioconductor views Annotation CpGIsland Sequencing Visualization
Date of publicationNone
MaintainerAltuna Akalin <aakalin@gmail.com>, Vedran Franke <vedran.franke@gmail.com>
LicenseArtistic-2.0
Version1.8.0
http://bioinformatics.mdc-berlin.de/genomation/

View on Bioconductor

Man pages

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...

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...

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

cage: Example CAGE data set.

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

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.

findFeatureComb-methods: Find combitations of genomic features

genes: Example RefSeq genes data set.

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

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

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

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...

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

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-ScoreMatrix-ANY-ANY-method: Extract method for a ScoreMatrix object.

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

Functions

annotateWithFeature Man page
annotateWithFeatureFlank Man page
annotateWithFeatureFlank,GRanges,GRanges,GRanges-method Man page
annotateWithFeature,GRanges,GRanges-method Man page
annotateWithFeatures Man page
annotateWithFeatures,GRanges,GRangesList-method Man page
annotateWithFeatures,GRangesList,GRangesList-method Man page
annotateWithGeneParts Man page
annotateWithGeneParts,GRanges,GRangesList-method Man page
annotateWithGeneParts,GRangesList,GRangesList-method Man page
AnnotationByFeature-class Man page
AnnotationByGeneParts-class Man page
AnnotationByGeneParts-method Man page
binMatrix Man page
binMatrix,ScoreMatrixList-method Man page
binMatrix,ScoreMatrix-method Man page
cage Man page
calculateOverlapSignificance Man page
calculateOverlapSignificance,GRanges,GRanges-method Man page
convertBed2Exons Man page
convertBed2Exons,data.frame-method Man page
convertBed2Introns Man page
convertBed2Introns,data.frame-method Man page
convertBedDf Man page
convertBedDf,data.frame-method Man page
cpgi Man page
extract,ScoreMatrix,ANY-method Man page
findFeatureComb Man page
findFeatureComb,GRangesList-method Man page
genes Man page
getAssociationWithTSS Man page
getAssociationWithTSS, Man page
getAssociationWithTSS,AnnotationByGeneParts-method Man page
getAssociationWithTSS,-methods Man page
getFeatsWithTargetsStats Man page
getFeatsWithTargetsStats,AnnotationByFeature-method Man page
getFlanks Man page
getFlanks,GRanges-method Man page
getMembers Man page
getMembers,AnnotationByFeature-method Man page
getRandomEnrichment Man page
getRandomEnrichment,GRanges,GRanges-method Man page
getTargetAnnotationStats Man page
getTargetAnnotationStats,AnnotationByFeature-method Man page
gffToGRanges Man page
heatMatrix Man page
heatMeta Man page
heatTargetAnnotation Man page
intersectScoreMatrixList Man page
intersectScoreMatrixList,ScoreMatrixList-method Man page
multiHeatMatrix Man page
Ops,numeric,ScoreMatrixList-method Man page
Ops,ScoreMatrixList,numeric-method Man page
Ops,ScoreMatrixList,ScoreMatrixList-method Man page
Ops,ScoreMatrix,ScoreMatrix-method Man page
orderBy Man page
orderBy,ScoreMatrixList-method Man page
patternMatrix Man page
patternMatrix,character,DNAStringSet,ANY-method Man page
patternMatrix,character,DNAStringSet-method Man page
patternMatrix,character,GRanges,BSgenome-method Man page
patternMatrix,list,DNAStringSet,ANY-method Man page
patternMatrix,list,DNAStringSet-method Man page
patternMatrix,list,GRanges,BSgenome-method Man page
patternMatrix,matrix,DNAStringSet,ANY-method Man page
patternMatrix,matrix,DNAStringSet-method Man page
patternMatrix,matrix,GRanges,BSgenome-method Man page
plotGeneAnnotation Man page
plotMeta Man page
plotTargetAnnotation Man page
plotTargetAnnotation,AnnotationByFeature-method Man page
promoters Man page
RandomEnrichment-class Man page
randomizeFeature Man page
randomizeFeature,GRanges-method Man page
readBed Man page
readBroadPeak Man page
readFeatureFlank Man page
readFeatureFlank,character-method Man page
readGeneric Man page
readNarrowPeak Man page
readTranscriptFeatures Man page
readTranscriptFeatures,character-method Man page
scaleScoreMatrix Man page
scaleScoreMatrixList Man page
scaleScoreMatrixList,ScoreMatrixList-method Man page
scaleScoreMatrix,ScoreMatrix-method Man page
ScoreMatrix Man page
[,ScoreMatrix,ANY,ANY,ANY-method Man page
[,ScoreMatrix,ANY,ANY-method Man page
ScoreMatrixBin Man page
ScoreMatrixBin,character,GRangesList-method Man page
ScoreMatrixBin,character,GRanges-method Man page
ScoreMatrixBin,GRanges,GRangesList-method Man page
ScoreMatrixBin,GRanges,GRanges-method Man page
ScoreMatrixBin,RleList,GRangesList-method Man page
ScoreMatrixBin,RleList,GRanges-method Man page
ScoreMatrix,character,GRanges-method Man page
ScoreMatrix-class Man page
ScoreMatrix,GRanges,GRanges-method Man page
ScoreMatrixList Man page
[,ScoreMatrixList,ANY,ANY,ANY-method Man page
ScoreMatrixList-class Man page
[,ScoreMatrixList-method Man page
[,ScoreMatrix-method Man page
ScoreMatrix,RleList,GRanges-method Man page
show,AnnotationByFeature-method Man page
show,AnnotationByGeneParts-method Man page
show,RandomEnrichment-method Man page
show,ScoreMatrixList-method Man page
show,ScoreMatrix-method Man page

Files

.Rinstignore
DESCRIPTION
NAMESPACE
NEWS
R
R/Ops.R R/deprecated_defunct.R R/documentData.R R/findFeatureComb.R R/genomation-classes.R R/getRandomEnrichment.R R/patternMatrix.R R/plotMatrix.R R/randomizeFeature.R R/readAnnotate.R R/readData.R R/scoreMatrix.R R/scoreMatrixBin.R R/scoreMatrixList.R R/test_genomation_package.R
README.md
build
build/vignette.rds
data
data/cage.RData
data/cpgi.RData
data/genes.RData
data/promoters.RData
inst
inst/CITATION
inst/doc
inst/doc/Figures
inst/doc/GenomationManual.R
inst/doc/GenomationManual.Rmd
inst/doc/GenomationManual.html
inst/extdata
inst/extdata/EnhancersEncode.txt.Test
inst/extdata/Fantom4.Cage.Test
inst/extdata/chr21.CpGi.hg19.bed
inst/extdata/chr21.refseq.hg19.bed
inst/extdata/chr21.refseq.hg19.gtf
inst/extdata/ex.broadPeak
inst/extdata/ex.narrowPeak
inst/extdata/tab1.bed
inst/extdata/tab2.bed
inst/extdata/tab3.bed
inst/scripts
inst/scripts/FunctionNames.txt
inst/scripts/devtools_test.R inst/scripts/produceDataForExamples.R
inst/tests
inst/unitTests
inst/unitTests/tab.test1
inst/unitTests/tab.test2
inst/unitTests/tab.test3
inst/unitTests/tab.test3.zip
inst/unitTests/tab.test4
inst/unitTests/test.bam
inst/unitTests/test.bam.bai
inst/unitTests/test.bedGraph
inst/unitTests/test.bw
inst/unitTests/test.gtf
inst/unitTests/test_PatternMatrix.R inst/unitTests/test_ScoreMatrix.R inst/unitTests/test_ScoreMatrixBin.R inst/unitTests/test_ScoreMatrixList.R
inst/unitTests/test_pairedend.bam
inst/unitTests/test_pairedend.bam.bai
inst/unitTests/test_readData.R
man
man/AnnotationByFeature-class.Rd man/AnnotationByGeneParts-class.Rd man/AnnotationByGeneParts-methods.Rd man/Ops-ScoreMatrix-ScoreMatrix-method.Rd man/Ops-ScoreMatrixList-ScoreMatrixList-method.Rd man/Ops-ScoreMatrixList-numeric-method.Rd man/Ops-numeric-ScoreMatrixList-method.Rd man/RandomEnrichment-class.Rd man/ScoreMatrix-class.Rd man/ScoreMatrix-methods.Rd man/ScoreMatrixBin-methods.Rd man/ScoreMatrixList-class.Rd man/ScoreMatrixList-methods.Rd man/annotateWithFeature-methods.Rd man/annotateWithFeatureFlank-methods.Rd man/annotateWithFeatures-methods.Rd man/annotateWithGeneParts-methods.Rd man/binMatrix-methods.Rd man/cage.Rd man/calculateOverlapSignificance-methods.Rd man/convertBed2Exons-methods.Rd man/convertBed2Introns-methods.Rd man/convertBedDf-methods.Rd man/cpgi.Rd man/findFeatureComb-methods.Rd man/genes.Rd man/getFeatsWithTargetsStats-methods.Rd man/getFlanks-methods.Rd man/getMembers-methods.Rd man/getRandomEnrichment-methods.Rd man/getTargetAnnotationStats-methods.Rd man/gffToGRanges.Rd man/heatMatrix.Rd man/heatMeta.Rd man/heatTargetAnnotation-methods.Rd man/intersectScoreMatrixList-methods.Rd man/multiHeatMatrix.Rd man/orderBy-methods.Rd man/patternMatrix-methods.Rd man/plotMeta.Rd man/plotTargetAnnotation-methods.Rd man/promoters.Rd man/randomizeFeature-methods.Rd man/readBed.Rd man/readBroadPeak.Rd man/readFeatureFlank-methods.Rd man/readGeneric.Rd man/readNarrowPeak.Rd man/readTranscriptFeatures-methods.Rd man/scaleScoreMatrix-methods.Rd man/scaleScoreMatrixList.Rd man/show-methods.Rd man/sub-ScoreMatrix-ANY-ANY-ANY-method.Rd man/sub-ScoreMatrix-ANY-ANY-method.Rd man/sub-ScoreMatrixList-ANY-ANY-ANY-method.Rd
tests
tests/genomation_unit_tests.R
vignettes
vignettes/Figures
vignettes/Figures/ctcfScoreMatrixList-1.png
vignettes/Figures/genomationFlowChart1.png
vignettes/Figures/heatMatrix1-1.png
vignettes/Figures/heatMatrix1-2.png
vignettes/Figures/heatMatrix2-1.png
vignettes/Figures/heatMatrixScales-1.png
vignettes/Figures/multiHeatMatrix1-1.png
vignettes/Figures/multiHeatMatrix2-1.png
vignettes/Figures/plotGeneAnnotation-1.png
vignettes/Figures/plotGeneAnnotation-2.png
vignettes/Figures/plotScaledProfile-1.png
vignettes/Figures/visualizeFeatureComb-1.png
vignettes/GenomationManual-knitr.html
vignettes/GenomationManual.Rmd
vignettes/cache

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