Package: CAGEfightR 1.27.0
Malte Thodberg
CAGEfightR: Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor
CAGE is a widely used high throughput assay for measuring transcription start site (TSS) activity. CAGEfightR is an R/Bioconductor package for performing a wide range of common data analysis tasks for CAGE and 5'-end data in general. Core functionality includes: import of CAGE TSSs (CTSSs), tag (or unidirectional) clustering for TSS identification, bidirectional clustering for enhancer identification, annotation with transcript and gene models, correlation of TSS and enhancer expression, calculation of TSS shapes, quantification of CAGE expression as expression matrices and genome brower visualization.
Authors:
CAGEfightR_1.27.0.tar.gz
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CAGEfightR.pdf |CAGEfightR.html✨
CAGEfightR/json (API)
NEWS
| # Install 'CAGEfightR' in R: |
| install.packages('CAGEfightR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/maltethodberg/cagefightr/issues
- exampleBidirectional - Example CAGE Data
- exampleCTSSs - Example CAGE Data
- exampleDesign - Example CAGE Data
- exampleGenes - Example CAGE Data
- exampleUnidirectional - Example CAGE Data
On BioConductor:CAGEfightR-1.27.0(bioc 3.21)CAGEfightR-1.26.0(bioc 3.20)
softwaretranscriptioncoveragegeneexpressiongeneregulationpeakdetectiondataimportdatarepresentationtranscriptomicssequencingannotationgenomebrowsersnormalizationpreprocessingvisualization
Last updated 23 days agofrom:5e8f35bfdd. Checks:ERROR: 1 WARNING: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | FAIL | Nov 18 2024 |
| R-4.5-win | WARNING | Nov 18 2024 |
| R-4.5-linux | WARNING | Nov 18 2024 |
| R-4.4-win | WARNING | Nov 18 2024 |
| R-4.4-mac | WARNING | Nov 18 2024 |
| R-4.3-win | WARNING | Nov 18 2024 |
| R-4.3-mac | WARNING | Nov 18 2024 |
Exports:assignGeneIDassignMissingIDassignTxIDassignTxTypebalanceBCbalanceDbwCommonGenomebwGenomeCompatibilitybwValidcalcBidirectionalitycalcCompositioncalcPooledcalcShapecalcSupportcalcTotalTagscalcTPMcheckCTSSscheckPeakedcheckPooledclusterBidirectionallyclusterUnidirectionallycombineClustersconvertBAM2BigWigconvertBED2BedGraphconvertBED2BigWigconvertBedGraph2BEDconvertBedGraph2BigWigconvertBigWig2BEDconvertBigWig2BedGraphconvertGRanges2GPosfindLinksfindStretchesquantifyClustersquantifyCTSSsquantifyGenesquickEnhancersquickGenesquickTSSsshapeEntropyshapeIQRshapeMeansubsetByBidirectionalitysubsetByCompositionsubsetBySupportswapRangesswapScorestrackBalancetrackClusterstrackCTSStrackLinkstrimToPeaktrimToPercentilestuneTagClusteringutilsAggregateRowsutilsDeStrandutilsScoreOverlapsutilsSimplifyTxDb
Dependencies:abindAnnotationDbiAnnotationFilteraskpassassertthatbackportsbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcheckmatecliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArraydeldirdichromatdigestdplyrensembldbevaluatefansifarverfastmapfilelockfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicFilesGenomicInteractionsGenomicRangesggplot2gluegridExtragtableGvizhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2igraphInteractionSetinterpIRangesisobandjpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelatticeExtralazyevallifecyclelobstrmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmennetopensslpillarpkgconfigplogrpngprettyunitsprogressProtGenericspryrpurrrR6rappdirsRColorBrewerRcppRcppEigenRCurlrestfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalessnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitewithrxfunXMLxml2XVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Annotate ranges with gene ID. | assignGeneID assignGeneID,GenomicRanges,GenomicRanges-method assignGeneID,GenomicRanges,TxDb-method assignGeneID,RangedSummarizedExperiment,GenomicRanges-method assignGeneID,RangedSummarizedExperiment,TxDb-method |
| Annotate ranges with missing IDs. | assignMissingID assignMissingID,character-method assignMissingID,GenomicRanges-method assignMissingID,RangedSummarizedExperiment-method |
| Annotate ranges with transcript ID. | assignTxID assignTxID,GenomicRanges,GenomicRanges-method assignTxID,GenomicRanges,TxDb-method assignTxID,RangedSummarizedExperiment,GenomicRanges-method assignTxID,RangedSummarizedExperiment,TxDb-method |
| Annotate ranges with transcript type. | assignTxType assignTxType,GenomicRanges,GenomicRangesList-method assignTxType,GenomicRanges,TxDb-method assignTxType,RangedSummarizedExperiment,GenomicRangesList-method assignTxType,RangedSummarizedExperiment,TxDb-method |
| Balance statistic: Bhattacharyya coefficient (BC) | balanceBC |
| Balance statistic: Andersson's D. | balanceD |
| Find a common genome for a series of BigWig files. | bwCommonGenome |
| Check if BigWig-files are compatible with a given genome. | bwGenomeCompatibility |
| Check if BigWig-files are valid. | bwValid bwValid,BigWigFile-method bwValid,BigWigFileList-method |
| Calculate sample-wise bidirectionally of clusters. | calcBidirectionality calcBidirectionality,GPos-method calcBidirectionality,GRanges-method calcBidirectionality,RangedSummarizedExperiment-method |
| Calculate composition of CAGE data. | calcComposition |
| Calculate pooled expression across all samples. | calcPooled |
| Calculate Tag Cluster shapes | calcShape calcShape,GRanges,GPos-method calcShape,GRanges,GRanges-method calcShape,GRanges,RangedSummarizedExperiment-method calcShape,RangedSummarizedExperiment,GRanges-method calcShape,RangedSummarizedExperiment,RangedSummarizedExperiment-method |
| Calculate support of CAGE data. | calcSupport |
| Calculate the total number of CAGE tags across samples. | calcTotalTags |
| Calculate CAGE Tags-Per-Million (TPM) | calcTPM |
| Helper for checking files containing CTSSs | checkCTSSs checkCTSSs,ANY-method checkCTSSs,BigWigFile-method checkCTSSs,character-method checkCTSSs,GPos-method checkCTSSs,GRanges-method |
| Helper for checking cluster with peaks | checkPeaked |
| Helper for checking pooled signal | checkPooled |
| Bidirectional clustering of pooled CTSSs. | clusterBidirectionally clusterBidirectionally,GPos-method clusterBidirectionally,GRanges-method clusterBidirectionally,RangedSummarizedExperiment-method |
| Unidirectional Clustering (Tag Clustering) of pooled CTSSs. | clusterUnidirectionally clusterUnidirectionally,GPos-method clusterUnidirectionally,GRanges-method clusterUnidirectionally,RangedSummarizedExperiment-method |
| Combine two CAGE experiments. | combineClusters combineClusters,RangedSummarizedExperiment,RangedSummarizedExperiment-method |
| Extract CTSSs from BAM-files (EXPERIMENTAL) | convertBAM2BigWig |
| Convert CTSSs stored in different file formats. | convertBED2BedGraph convertBED2BigWig convertBedGraph2BED convertBedGraph2BigWig convertBigWig2BED convertBigWig2BedGraph |
| Convert GRanges with scores to GPos | convertGRanges2GPos |
| Example CAGE Data | exampleBidirectional exampleCTSSs exampleDesign exampleGenes exampleUnidirectional |
| Find nearby pairs of clusters and calculate pairwise correlations. | findLinks findLinks,GRanges-method findLinks,RangedSummarizedExperiment-method |
| Find stretches of clusters | findStretches findStretches,GRanges-method findStretches,RangedSummarizedExperiment-method |
| Quantify expression of clusters (TSSs or enhancers) by summing CTSSs within clusters. | quantifyClusters |
| Quantify CAGE Transcriptions Start Sites (CTSSs) | quantifyCTSSs quantifyCTSSs,BigWigFileList,BigWigFileList-method quantifyCTSSs,character,character-method |
| Quantify CAGE Transcriptions Start Sites (CTSSs) | quantifyCTSSs2 |
| Quantify expression of genes | quantifyGenes |
| Identify and quantify enhancers. | quickEnhancers |
| Identify and quantify genes. | quickGenes |
| Identify and quantify Transcription Start Sites (TSSs). | quickTSSs |
| Shape statistic: Shannon Entropy | shapeEntropy |
| Shape statitic: Interquartile range | shapeIQR |
| Shape statistic: Mean | shapeMean |
| Shape statistic: Multimodality | shapeMultimodality |
| Subset by sample-wise bidirectionality of clusters. | subsetByBidirectionality subsetByBidirectionality,GPos-method subsetByBidirectionality,GRanges-method subsetByBidirectionality,RangedSummarizedExperiment-method |
| Subset by composition across samples | subsetByComposition |
| Subset by support across samples | subsetBySupport |
| Swap ranges in a GRanges. | swapRanges swapRanges,GenomicRanges-method swapRanges,RangedSummarizedExperiment-method |
| Swap scores in SummarizedExperiment | swapScores |
| Create Genome Browser Track of bidirectional balance scores | trackBalance trackBalance,GPos-method trackBalance,GRanges-method trackBalance,RangedSummarizedExperiment-method |
| Create genome browser track of clusters. | trackClusters trackClusters,GRanges-method trackClusters,RangedSummarizedExperiment-method |
| Create Genome Browser track of CTSSs. | trackCTSS trackCTSS,GPos-method trackCTSS,GRanges-method trackCTSS,RangedSummarizedExperiment-method |
| Create a genome browser track of links. | trackLinks |
| Trim width of TCs by distance from TC peak | trimToPeak trimToPeak,GRanges,GPos-method trimToPeak,GRanges,GRanges-method trimToPeak,GRanges,RangedSummarizedExperiment-method trimToPeak,RangedSummarizedExperiment,GenomicRanges-method trimToPeak,RangedSummarizedExperiment,RangedSummarizedExperiment-method |
| Trim width of TCs to expression percentiles | trimToPercentiles trimToPercentiles,GRanges,GPos-method trimToPercentiles,GRanges,GRanges-method trimToPercentiles,GRanges,RangedSummarizedExperiment-method trimToPercentiles,RangedSummarizedExperiment,GenomicRanges-method trimToPercentiles,RangedSummarizedExperiment,RangedSummarizedExperiment-method |
| Determine the optimal pooled threshold for unidirectional tag clustering. | tuneTagClustering tuneTagClustering,GPos-method tuneTagClustering,GRanges-method tuneTagClustering,RangedSummarizedExperiment-method |
| Utility: Aggregate rows | utilsAggregateRows utilsAggregateRows,dgCMatrix-method utilsAggregateRows,matrix-method |
| Utility: Split Genomic Ranges by strand | utilsDeStrand |
| Utility: Counting overlaps taking into account scores | utilsScoreOverlaps |
| Utility: Extract annotation hierachy from a TxDb. | utilsSimplifyTxDb |
