Package: genomation 1.45.0

Altuna Akalin

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.

Authors:Altuna Akalin [aut, cre], Vedran Franke [aut, cre], Katarzyna Wreczycka [aut], Alexander Gosdschan [ctb], Liz Ing-Simmons [ctb], Bozena Mika-Gospodorz [ctb]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
genomation/json (API)

# Install 'genomation' in R:

install.packages('genomation', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bimsbbioinfo/genomation/issues

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

cage - Example CAGE data set.
cpgi - Example CpG island data set.
genes - Example RefSeq genes data set.
promoters - Example promoter data set.

On BioConductor:genomation-1.45.0(bioc 3.24)genomation-1.44.0(bioc 3.23)

annotation sequencing visualization cpgisland cpp

11.33 score 80 stars 5 packages 784 scripts 17 mentions 75 exports 91 dependencies

Last updated from:df3461e628. Checks:1 ERROR, 11 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	208
linux-devel-arm64	NOTE	370
linux-devel-x86_64	NOTE	498
source / vignettes	OK	344
linux-release-arm64	NOTE	358
linux-release-x86_64	NOTE	451
macos-release-arm64	NOTE	272
macos-release-x86_64	NOTE	519
macos-oldrel-arm64	NOTE	369
macos-oldrel-x86_64	NOTE	678
windows-devel	NOTE	379
windows-release	NOTE	383
windows-oldrel	NOTE	376
wasm-release	OK	433

Exports:annotateWithFeature annotateWithFeatureFlank annotateWithFeatures annotateWithGeneParts annotatGrWithGeneParts bed12ToExons bed12ToIntrons binMatrix binMax binMean binMedian binMin binner binSum c.ScoreMatrix c.ScoreMatrixList calculateOverlapSignificance checkBedValidity checkClass compressedAndUrl2temp constrainRanges convertBed2Exons convertBed2Introns convertBedDf detectUCSCheader distance2NearestFeature enrichmentMatrix file.ext findFeatureComb galpTo2Ranges getAssociationWithTSS getColors getFeatsWithTargetsStats getFlanks getMembers getRandomEnrichment getTargetAnnotationStats gffToGRanges heatMatrix heatMeta heatTargetAnnotation intersectScoreMatrixList listSliceMax listSliceMean listSliceMedian listSliceMin listSliceSum Max_c Mean_c Median_c Min_c multiHeatMatrix orderBy patternMatrix plotGeneAnnotation plotMeta plotTargetAnnotation randomizeFeature read.zip readBam readBed readBigWig readBroadPeak readFeatureFlank readGeneric readNarrowPeak readTableFast readTranscriptFeatures scaleScoreMatrix scaleScoreMatrixList ScoreMatrix ScoreMatrixBin ScoreMatrixList Sum_c target.type

Dependencies:abind askpass BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops BSgenome cigarillo cli clipr codetools cpp11 crayon curl data.table DelayedArray farver formatR futile.logger futile.options generics GenomicAlignments GenomicRanges ggplot2 glue gridBase gtable hms httr impute IRanges isoband jsonlite KernSmooth labeling lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats mime openssl pillar pkgconfig plotrix plyr prettyunits progress R6 RColorBrewer Rcpp RCurl readr reshape2 restfulr Rhtslib rjson rlang Rsamtools rtracklayer S4Arrays S4Vectors S7 scales Seqinfo seqPattern snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyselect tzdb utf8 vctrs viridisLite vroom withr XML XVector yaml

genomation: a toolkit for annotation and visualization of genomic data

Rendered fromGenomationManual.Rmdusingknitr::rmarkdown

Last update: 2018-08-30
Started: 2016-10-05

Help page	Topics
Extract method for a ScoreMatrix object.	[,ScoreMatrix,ANY,ANY,ANY-method [,ScoreMatrix-method
Extract method for a ScoreMatrixList object.	[,ScoreMatrixList,ANY,ANY,ANY-method [,ScoreMatrixList-method
Function to annotate given GRanges object with a given genomic feature	annotateWithFeature annotateWithFeature,GRanges,GRanges-method
Function to annotate a given GRanges object with promoter,exon,intron & intergenic values	annotateWithFeatureFlank annotateWithFeatureFlank,GRanges,GRanges,GRanges-method
Annotate given ranges with genomic features	annotateWithFeatures annotateWithFeatures,GRanges,GRangesList-method annotateWithFeatures,GRangesList,GRangesList-method
Annotate given object with promoter, exon, intron and intergenic regions	annotateWithGeneParts annotateWithGeneParts,GRanges,GRangesList-method annotateWithGeneParts,GRangesList,GRangesList-method
An S4 class that information on overlap of target features with annotation features	AnnotationByFeature-class
An S4 class that information on overlap of target features with annotation features	AnnotationByGeneParts-class
Bins the columns of a matrix using a user provided function	binMatrix binMatrix,ScoreMatrix-method binMatrix,ScoreMatrixList-method
c.ScoreMatrix	c.ScoreMatrix
c.ScoreMatrixList	c.ScoreMatrixList
Example CAGE data set.	cage
function that calculates the significance of overlaps of two sets of features using randomization	calculateOverlapSignificance calculateOverlapSignificance,GRanges,GRanges-method
convert a data frame read-in from a bed file to a GRanges object for exons	convertBed2Exons convertBed2Exons,data.frame-method
convert a data frame read-in from a bed file to a GRanges object for introns	convertBed2Introns convertBed2Introns,data.frame-method
convert a data frame read-in from a bed file to a GRanges object	convertBedDf convertBedDf,data.frame-method
Example CpG island data set.	cpgi
Compute an enrichment of IP over control both stored in ScoreMatrix objects	enrichmentMatrix enrichmentMatrix,ScoreMatrix,ScoreMatrix-method
Compute an enrichment of IP (stored in ScoreMatrixList object) over control (stored in ScoreMatrix object)	enrichmentMatrix,ScoreMatrixList,ScoreMatrix-method
Compute an enrichment of IP over control both stored in ScoreMatrixList objects	enrichmentMatrix,ScoreMatrixList,ScoreMatrixList-method
Find combitations of genomic features	findFeatureComb findFeatureComb,GRangesList-method
Example RefSeq genes data set.	genes
Get distance to nearest TSS and gene id from AnnotationByGeneParts	AnnotationByGeneParts-method getAssociationWithTSS getAssociationWithTSS, getAssociationWithTSS,-methods getAssociationWithTSS,AnnotationByGeneParts-method
Get the percentage/count of annotation features overlapping with target features from AnnotationByFeature	getFeatsWithTargetsStats getFeatsWithTargetsStats,AnnotationByFeature-method
Function to get upstream and downstream adjecent regions to a genomic feature such as CpG islands	getFlanks getFlanks,GRanges-method
Get the membership slot of AnnotationByFeature	getMembers getMembers,AnnotationByFeature-method
get enrichment based on randomized feature overlap	getRandomEnrichment getRandomEnrichment,GRanges,GRanges-method
Get the percentage of target features overlapping with annotation from AnnotationByFeature	getTargetAnnotationStats getTargetAnnotationStats,AnnotationByFeature-method
Converts a gff formated data.frame into a GenomicRanges object. The GenomicRanges object needs to be properly formated for the function to work.	gffToGRanges
Draw a heatmap of a given ScoreMatrix object	heatMatrix
Heatmap for meta-region profiles	heatMeta
Plots the percentage of overlapping intervals with genomic features in a heatmap	heatTargetAnnotation plotGeneAnnotation
Get common rows from all matrices in a ScoreMatrixList object	intersectScoreMatrixList intersectScoreMatrixList,ScoreMatrixList-method
Draw multiple heatmaps from a ScoreMatrixList object	multiHeatMatrix
Ops method for a ScoreMatrixList object. It enables to use arithmetic, indicator and logic operations on ScoreMatrixList objects.	Ops,numeric,ScoreMatrixList-method
Ops method for a ScoreMatrix object. It enables to use arithmetic, indicator and logic operations on ScoreMatrix objects.	Ops,ScoreMatrix,ScoreMatrix-method
Ops method for a ScoreMatrixList object. It enables to use arithmetic, indicator and logic operations on ScoreMatrixList objects.	Ops,ScoreMatrixList,numeric-method
Ops method for a ScoreMatrixList object. It enables to use arithmetic, indicator and logic operations on ScoreMatrixList objects.	Ops,ScoreMatrixList,ScoreMatrixList-method
Reorder all elements of a ScoreMatrixList to a given ordering vector	orderBy orderBy,ScoreMatrixList-method
Get scores that correspond to k-mer or PWM matrix occurrence for bases in each window	patternMatrix patternMatrix,character,DNAStringSet,ANY-method patternMatrix,character,DNAStringSet-method patternMatrix,character,GRanges,BSgenome-method patternMatrix,list,DNAStringSet,ANY-method patternMatrix,list,DNAStringSet-method patternMatrix,list,GRanges,BSgenome-method patternMatrix,matrix,DNAStringSet,ANY-method patternMatrix,matrix,DNAStringSet-method patternMatrix,matrix,GRanges,BSgenome-method
Line plot(s) for meta-region profiles	plotMeta
Plot annotation categories from AnnotationByGeneParts or AnnotationByFeature	plotTargetAnnotation plotTargetAnnotation,AnnotationByFeature-method
Example promoter data set.	promoters
An S4 class for storing 'getRandomEnrichment' function results	RandomEnrichment-class
function that randomizes the genomic coordinates	randomizeFeature randomizeFeature,GRanges-method
Read a BED file and convert it to GRanges.	readBed
A function to read the Encode formatted broad peak file into a GRanges object	readBroadPeak
A function to read-in genomic features and their upstream and downstream adjecent regions such as CpG islands and their shores	readFeatureFlank readFeatureFlank,character-method
Read a tabular file and convert it to GRanges.	readGeneric
A function to read the Encode formatted narrowPeak file into a GRanges object	readNarrowPeak
Function for reading exon intron and promoter structure from a given bed file	readTranscriptFeatures readTranscriptFeatures,character-method
Scales the values in the matrix by rows and/or columns	scaleScoreMatrix scaleScoreMatrix,ScoreMatrix-method
Scale the ScoreMatrixList	scaleScoreMatrixList scaleScoreMatrixList,ScoreMatrixList-method
Get base-pair score for bases in each window	ScoreMatrix ScoreMatrix,character,GRanges-method ScoreMatrix,GRanges,GRanges-method ScoreMatrix,RleList,GRanges-method
An S4 class for storing 'ScoreMatrix' function results	ScoreMatrix-class
Get bin score for bins on each window	ScoreMatrixBin ScoreMatrixBin,character,GRanges-method ScoreMatrixBin,character,GRangesList-method ScoreMatrixBin,GRanges,GRanges-method ScoreMatrixBin,GRanges,GRangesList-method ScoreMatrixBin,RleList,GRanges-method ScoreMatrixBin,RleList,GRangesList-method
Make ScoreMatrixList from multiple targets	ScoreMatrixList
An S4 class for storing a set of 'ScoreMatrixList'	ScoreMatrixList-class
show method for some of the genomation classes	show,AnnotationByFeature-method show,AnnotationByGeneParts-method show,RandomEnrichment-method show,ScoreMatrix-method show,ScoreMatrixList-method

Package: genomation 1.45.0

genomation: Summary, annotation and visualization of genomic data

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