Package: CAGEr 2.13.0
Charles Plessy
CAGEr: Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining
The _CAGEr_ package identifies transcription start sites (TSS) and their usage frequency from CAGE (Cap Analysis Gene Expression) sequencing data. It normalises raw CAGE tag count, clusters TSSs into tag clusters (TC) and aggregates them across multiple CAGE experiments to construct consensus clusters (CC) representing the promoterome. CAGEr provides functions to profile expression levels of these clusters by cumulative expression and rarefaction analysis, and outputs the plots in ggplot2 format for further facetting and customisation. After clustering, CAGEr performs analyses of promoter width and detects differential usage of TSSs (promoter shifting) between samples. CAGEr also exports its data as genome browser tracks, and as R objects for downsteam expression analysis by other Bioconductor packages such as DESeq2, CAGEfightR, or seqArchR.
Authors:
CAGEr_2.13.0.tar.gz
CAGEr_2.13.0.zip(r-4.5)CAGEr_2.13.0.zip(r-4.4)CAGEr_2.13.0.zip(r-4.3)
CAGEr_2.13.0.tgz(r-4.4-any)CAGEr_2.13.0.tgz(r-4.3-any)
CAGEr_2.13.0.tar.gz(r-4.5-noble)CAGEr_2.13.0.tar.gz(r-4.4-noble)
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CAGEr.pdf |CAGEr.html✨
CAGEr/json (API)
NEWS
| # Install 'CAGEr' in R: |
| install.packages('CAGEr', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- FANTOM5humanSamples - FANTOM5 human samples
- FANTOM5mouseSamples - FANTOM5 mouse samples
- exampleCAGEexp - Example CAGEexp object.
- exampleZv9_annot - Example zebrafish annotation data
On BioConductor:CAGEr-2.13.0(bioc 3.21)CAGEr-2.12.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
preprocessingsequencingnormalizationfunctionalgenomicstranscriptiongeneexpressionclusteringvisualization
Last updated 2 months agofrom:cdfe2b18c3. Checks:OK: 5 NOTE: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 29 2024 |
| R-4.5-win | NOTE | Nov 29 2024 |
| R-4.5-linux | NOTE | Nov 29 2024 |
| R-4.4-win | OK | Nov 29 2024 |
| R-4.4-mac | OK | Nov 29 2024 |
| R-4.3-win | OK | Nov 29 2024 |
| R-4.3-mac | OK | Nov 29 2024 |
Exports:.ctss_summary_for_clustersaggregateTagClustersannotateConsensusClustersannotateCTSSannotateTagClustersCAGEexpcoerceconsensusClustersDESeq2consensusClustersGRconsensusClustersGR<-consensusClustersSEconsensusClustersSE<-consensusClustersTpmCTSSCTSScoordinatesGRCTSScoordinatesGR<-CTSScumulativesCCCTSScumulativesTagClustersCTSSnormalizedTpmDFCTSSnormalizedTpmGRCTSStagCountDFCTSStagCountGRCTSStagCountSECTSStagCountSE<-CTSStoGenescumulativeCTSSdistributionCustomConsensusClustersdistcluexportToTrackexpressionClassesfilteredCTSSidxfilterLowExpCTSSfindStrandInvadersflagByUpstreamSequencesflagLowExpCTSSGeneExpDESeq2GeneExpSEgenomeNamegenomeName<-getCTSSgetExpressionProfilesgetShiftingPromotershanabihanabiPlotimportPublicDatainputFilesinputFiles<-inputFilesTypeinputFilesType<-librarySizesmergeCAGEsetsmergeSamplesnormalizeTagCountparacluplotAnnotplotCorrelationplotCorrelation2plotExpressionProfilesplotInterquantileWidthplotReverseCumulativesquantilePositionsquickEnhancersremoveStrandInvadersresetCAGEexpsampleLabelssampleLabels<-sampleListscoreShiftseqNameTotalsSEsetColorssummariseChrExprtagClustersGRTSSlogo
Dependencies:abindAnnotationDbiAnnotationFilteraskpassassertthatbackportsbase64encBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemCAGEfightRcheckmatecliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArraydeldirdichromatdigestdplyrensembldbevaluatefansifarverfastmapfilelockfontawesomeforeignformatRFormulaformula.toolsfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicFilesGenomicInteractionsGenomicRangesggplot2gluegridExtragtablegtoolsGvizhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2igraphInteractionSetinterpIRangesisobandjpegjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlatticelatticeExtralazyevallifecyclelobstrmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeMultiAssayExperimentmunsellnlmennetopenssloperator.toolspermutepillarpkgconfigplogrplyrpngprettyunitsprogressProtGenericspryrpurrrR6rappdirsRColorBrewerRcppRcppEigenRCurlreshape2restfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalessnowsomSparseArraystringdiststringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8VariantAnnotationvctrsveganVGAMviridisviridisLitewithrxfunXMLxml2XVectoryamlzlibbioc
CAGEr: an R package for CAGE (Cap Analysis of Gene Expression) data analysis and promoterome mining
Rendered fromCAGEexp.Rmdusingknitr::rmarkdownon Nov 29 2024.Last update: 2024-05-24
Started: 2017-12-04
Use of CAGE resources with CAGEr
Rendered fromCAGE_Resources.Rmdusingknitr::rmarkdownon Nov 29 2024.Last update: 2024-05-10
Started: 2018-12-12
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Apply functions to identical CTSSes. | .byCtss .byCtss,data.table-method |
| Summarise CTSSs included in clusters | .ctss_summary_for_clusters |
| Get quantile positions | .get.quant.pos |
| .powerLaw | .powerLaw |
| Aggregate TCs across all samples | aggregateTagClusters aggregateTagClusters,CAGEr-method |
| Annotate and compute summary statistics | annotateConsensusClusters annotateConsensusClusters,CAGEexp,GRanges-method annotateConsensusClusters,CAGEexp,TxDb-method annotateCTSS annotateCTSS,CAGEexp,GRanges-method annotateCTSS,CAGEexp,TxDb-method annotateTagClusters annotateTagClusters,CAGEexp,GRanges-method annotateTagClusters,CAGEexp,TxDb-method |
| bam2CTSS | bam2CTSS |
| CAGEr class to hold all data and metadata about one CAGE experiment. | CAGEexp CAGEexp-class coerce,data.frame,CAGEexp-method |
| Multicore support in CAGEr | CAGEr_Multicore |
| CAGEr objects | CAGEr-class |
| coerceInBSgenome | coerceInBSgenome |
| ConsensusClusters | .ConsensusClusters ConsensusClusters ConsensusClusters-class |
| Set consensus clusters from CAGEr objects | consensusClusters<- consensusClustersGR<- consensusClustersGR<-,CAGEexp-method consensusClustersSE<- consensusClustersSE<-,CAGEexp,RangedSummarizedExperiment-method |
| Export _consensus cluster_ expression data for DESeq2 analysis | consensusClustersDESeq2 consensusClustersDESeq2,CAGEexp-method |
| Get consensus clusters from CAGEr objects | consensusClustersGR consensusClustersGR,CAGEexp-method consensusClustersSE consensusClustersSE,CAGEexp-method |
| Quantile metadata stored in CAGEr objects. | consensusClustersQuantile consensusClustersQuantile,CAGEexp-method consensusClustersQuantileLow consensusClustersQuantileLow,CAGEexp-method consensusClustersQuantileLow<- consensusClustersQuantileUp consensusClustersQuantileUp,CAGEexp-method consensusClustersQuantileUp<- |
| Extracting consensus clusters tpm matrix from CAGEr object | consensusClustersTpm consensusClustersTpm,CAGEexp-method |
| CAGE Transcription Start Sites | coerce,CTSS,GRanges-method coerce,GRanges,CTSS-method CTSS CTSS-class initialize,CTSS-method show,CTSS-method |
| Genomic coordinates of TSSs from a 'CAGEr' object | CTSScoordinatesGR CTSScoordinatesGR,CAGEexp-method CTSScoordinatesGR<- CTSScoordinatesGR<-,CAGEexp-method CTSStagCountSE<- CTSStagCountSE<-,CAGEexp-method |
| Get/set CTSS cumulative TC or CC data | CTSScumulativesCC CTSScumulativesCC,CAGEexp-method CTSScumulativesTagClusters CTSScumulativesTagClusters,CAGEexp-method CTSScumulativesTagClusters<- CTSScumulativesTagClusters<-,CAGEexp-method |
| Extracting normalized CAGE signal for TSSs from CAGEr objects | CTSSnormalizedTpmDF CTSSnormalizedTpmDF,CAGEexp-method CTSSnormalizedTpmGR CTSSnormalizedTpmGR,CAGEexp-method |
| Raw CAGE TSSs expression counts | CTSStagCountDF CTSStagCountDF,CAGEexp-method CTSStagCountGR CTSStagCountGR,CAGEexp-method CTSStagCountSE CTSStagCountSE,CAGEexp-method |
| Make a gene expression table. | CTSStoGenes CTSStoGenes,CAGEexp-method |
| Cumulative sums of CAGE counts along genomic regions | cumulativeCTSSdistribution cumulativeCTSSdistribution,CAGEexp-method |
| Expression levels of consensus cluster | CustomConsensusClusters CustomConsensusClusters,CAGEexp,GRanges-method |
| Distance clustering | distclu distclu,CAGEexp-method distclu,CTSS-method distclu,SummarizedExperiment-method |
| Example CAGEexp object. | exampleCAGEexp |
| Example zebrafish annotation data | exampleZv9_annot |
| Converts TSSs and clusters of TSSs to a genome browser track format | exportToTrack exportToTrack,CAGEexp-method exportToTrack,ConsensusClusters-method exportToTrack,CTSS-method exportToTrack,GRanges-method exportToTrack,GRangesList-method exportToTrack,TagClusters-method |
| Extract labels of _expression classes_ | expressionClasses expressionClasses,ConsensusClusters-method expressionClasses,CTSS-method |
| FANTOM5 human samples | FANTOM5humanSamples |
| FANTOM5 mouse samples | FANTOM5mouseSamples |
| The 'filteredCTSSidx()' function is in _CAGEr_ functions to retrieve the result of the 'flagLowExpCTSS()' function in a safe way. | filteredCTSSidx filteredCTSSidx,CAGEexp-method |
| Filter by upstream sequences | flagByUpstreamSequences flagByUpstreamSequences,ConsensusClusters-method flagByUpstreamSequences,CTSS-method flagByUpstreamSequences,GRanges-method flagByUpstreamSequences,TagClusters-method |
| Flag CTSSes based on sample expression | filterLowExpCTSS filterLowExpCTSS,CAGEr-method flagLowExpCTSS flagLowExpCTSS,CAGEr-method flagLowExpCTSS,DataFrame-method flagLowExpCTSS,matrix-method flagLowExpCTSS,RangedSummarizedExperiment-method |
| Export gene expression data for DESeq2 analysis | GeneExpDESeq2 GeneExpDESeq2,CAGEexp-method |
| Retreives the SummarizedExperiment containing gene expression levels. | GeneExpSE GeneExpSE,CAGEexp-method |
| Extracting genome name from CAGEr objects | genomeName genomeName,CAGEexp-method genomeName,CTSS-method genomeName<- genomeName<-,CAGEexp-method genomeName<-,CTSS-method |
| Reading CAGE data from input file(s) and detecting TSSs | getCTSS getCTSS,CAGEexp-method |
| CAGE data based expression clustering | getExpressionProfiles getExpressionProfiles,CAGEexp-method getExpressionProfiles,matrix-method |
| Select consensus clusters with shifting score above threshold | getShiftingPromoters getShiftingPromoters,CAGEexp-method |
| Calcultate richness in preparation for plotting | hanabi hanabi,GRanges-method hanabi,integer-method hanabi,List-method hanabi,list-method hanabi,matrix-method hanabi,numeric-method hanabi,Rle-method |
| Hanabi class | .hanabi hanabi-class |
| hanabiPlot | hanabiPlot |
| import.bam | import.bam |
| import.bam.ctss | import.bam.ctss |
| import.bedCTSS | import.bedCTSS |
| import.bedmolecule | import.bedmolecule |
| import.bedScore | import.bedScore |
| import.CAGEscanMolecule | import.CAGEscanMolecule |
| import.CTSS | import.CTSS |
| importPublicData | importPublicData importPublicData,character,character,ANY,character-method |
| Extracting paths to input files from CAGEr objects | inputFiles inputFiles,CAGEexp-method inputFiles<- inputFiles<-,CAGEexp-method |
| Input file formats for CAGEr objects | inputFilesType inputFilesType,CAGEexp-method inputFilesType<- inputFilesType<-,CAGEexp-method |
| Extracting library sizes from CAGEr objects | librarySizes librarySizes,CAGEexp-method |
| loadFileIntoGPos | loadFileIntoGPos |
| Process mapping statistics | mapStats |
| mapStats scopes | mapStatsScopes msScope_all msScope_annotation msScope_counts msScope_mapped msScope_qc msScope_steps |
| Merge two CAGEr objects into one | mergeCAGEsets mergeCAGEsets,CAGEexp,CAGEexp-method |
| Merge CAGE samples | mergeSamples mergeSamples,CAGEexp-method |
| moleculesGR2CTSS | moleculesGR2CTSS |
| Normalizing raw CAGE tag count | normalizeTagCount normalizeTagCount,CAGEexp-method |
| Parametric clustering | paraclu paraclu,CAGEexp-method paraclu,CTSS-method paraclu,GRanges-method paraclu,Pairs-method paraclu,SummarizedExperiment-method |
| parseCAGEscanBlocksToGrangeTSS | parseCAGEscanBlocksToGrangeTSS |
| Plotting Hanabi objects | lines.hanabi plot.hanabi points.hanabi |
| Plot annotation statistics | plotAnnot plotAnnot,CAGEexp-method plotAnnot,data.frame-method plotAnnot,DataFrame-method plotAnnot,GRangesList-method |
| Pairwise scatter plots and correlations of CAGE signal | plotCorrelation plotCorrelation,CAGEr-method plotCorrelation2 plotCorrelation2,CAGEexp-method plotCorrelation2,data.frame-method plotCorrelation2,DataFrame-method plotCorrelation2,matrix-method plotCorrelation2,SummarizedExperiment-method |
| Plot CAGE expression profiles | plotExpressionProfiles plotExpressionProfiles,CAGEexp-method |
| Plot cluster widths | plotInterquantileWidth plotInterquantileWidth,CAGEexp-method |
| Plot reverse cumulative number of CAGE tags per CTSS | plotReverseCumulatives plotReverseCumulatives,CAGEexp-method plotReverseCumulatives,GRanges-method plotReverseCumulatives,GRangesList-method |
| Determine CTSS quantile positions within clusters | quantilePositions quantilePositions,CAGEexp-method |
| Identify and quantify enhancers. | quickEnhancers quickEnhancers,CAGEexp-method |
| Hierarchical annotation of genomic regions. | ranges2annot |
| ranges2genes | ranges2genes |
| ranges2names | ranges2names |
| Reset a CAGEexp object | resetCAGEexp resetCAGEexp,CAGEexp-method |
| rowsum function for Rle DataFrames | rowsum.RleDataFrame |
| rowSums function for Rle DataFrames | rowSums.RleDataFrame |
| Get and set sample labels | sampleLabels sampleLabels,CAGEexp-method sampleLabels,CTSS-method sampleLabels<- sampleLabels<-,CAGEexp-method sampleLabels<-,CTSS-method sampleList sampleList,CAGEr-method |
| Calculate promoter shifting score | scoreShift scoreShift,CAGEexp-method |
| Retreives the SummarizedExperiment containing chromosome expression totals. | seqNameTotalsSE seqNameTotalsSE,CAGEexp-method seqNameTotalsSE<- |
| Set colors for samples | setColors setColors,CAGEr-method |
| Detect and remove strand invasion artefacts | findStrandInvaders findStrandInvaders,CAGEexp-method findStrandInvaders,CTSS-method removeStrandInvaders removeStrandInvaders,CAGEexp-method removeStrandInvaders,CTSS-method Strand invaders |
| Expression levels by chromosomes | summariseChrExpr summariseChrExpr,CAGEexp-method |
| TagClusters | .TagClusters TagClusters TagClusters-class |
| Extract tag clusters (TCs) for individual CAGE experiments | tagClustersGR tagClustersGR,CAGEexp-method tagClustersGR<- tagClustersGR<-,CAGEexp,ANY,TagClusters-method tagClustersGR<-,CAGEexp,missing,GRangesList-method |
| TSS logo | TSSlogo TSSlogo,CAGEexp-method TSSlogo,ConsensusClusters-method TSSlogo,CTSS-method TSSlogo,TagClusters-method |
