genomation: Summary, annotation and visualization of genomic data

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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.

Author
Altuna Akalin [aut, cre], Vedran Franke [aut, cre], Katarzyna Wreczycka [aut], Alexander Gosdschan [ctb], Liz Ing-Simmons [ctb]
Date of publication
None
Maintainer
Altuna Akalin <aakalin@gmail.com>, Vedran Franke <vedran.franke@gmail.com>
License
Artistic-2.0
Version
1.6.0
URLs

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