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.

AuthorAltuna Akalin [aut, cre], Vedran Franke [aut, cre], Katarzyna Wreczycka [aut], Alexander Gosdschan [ctb], Liz Ing-Simmons [ctb]
Date of publicationNone
MaintainerAltuna Akalin <aakalin@gmail.com>, Vedran Franke <vedran.franke@gmail.com>
LicenseArtistic-2.0
Version1.6.0
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...

idxStats: Fast retrieval of indexstats

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-method: Extract method for a ScoreMatrix object.

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

Files in this package

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

All documentation is copyright its authors; we didn't write any of that.