Package: CAGEfightR 1.33.0

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:Malte Thodberg

CAGEfightR_1.33.0.tar.gz
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CAGEfightR_1.33.0.tgz(r-4.6-any)CAGEfightR_1.33.0.tgz(r-4.5-any)
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
CAGEfightR/json (API)

# 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

Datasets:

exampleBidirectional - Example CAGE Data
exampleCTSSs - Example CAGE Data
exampleDesign - Example CAGE Data
exampleGenes - Example CAGE Data
exampleUnidirectional - Example CAGE Data

On BioConductor:CAGEfightR-1.33.0(bioc 3.24)CAGEfightR-1.32.0(bioc 3.23)

software transcription coverage geneexpression generegulation peakdetection dataimport datarepresentation transcriptomics sequencing annotation genomebrowsers normalization preprocessing visualization

8.24 score 10 stars 1 packages 129 scripts 608 downloads 6 mentions 57 exports 149 dependencies

Last updated from:e0241fa3c3. Checks:1 ERROR, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	264
linux-devel-x86_64	OK	589
source / vignettes	OK	516
linux-release-x86_64	OK	579
macos-release-arm64	OK	327
macos-oldrel-arm64	OK	343
windows-devel	OK	470
windows-release	OK	465
windows-oldrel	OK	458
wasm-release	OK	226

Exports:assignGeneID assignMissingID assignTxID assignTxType balanceBC balanceD bwCommonGenome bwGenomeCompatibility bwValid calcBidirectionality calcComposition calcPooled calcShape calcSupport calcTotalTags calcTPM checkCTSSs checkPeaked checkPooled clusterBidirectionally clusterUnidirectionally combineClusters convertBAM2BigWig convertBED2BedGraph convertBED2BigWig convertBedGraph2BED convertBedGraph2BigWig convertBigWig2BED convertBigWig2BedGraph convertGRanges2GPos findLinks findStretches quantifyClusters quantifyCTSSs quantifyGenes quickEnhancers quickGenes quickTSSs shapeEntropy shapeIQR shapeMean subsetByBidirectionality subsetByComposition subsetBySupport swapRanges swapScores trackBalance trackClusters trackCTSS trackLinks trimToPeak trimToPercentiles tuneTagClustering utilsAggregateRows utilsDeStrand utilsScoreOverlaps utilsSimplifyTxDb

Dependencies:abind AnnotationDbi AnnotationFilter askpass assertthat backports base64enc BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings biovizBase bit bit64 bitops blob BSgenome bslib cachem checkmate cigarillo cli cluster codetools colorspace cpp11 crayon curl data.table DBI dbplyr DelayedArray deldir dichromat digest dplyr ensembldb evaluate farver fastmap filelock fontawesome foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicFiles GenomicInteractions GenomicRanges ggplot2 glue gridExtra gtable Gviz highr Hmisc hms htmlTable htmltools htmlwidgets httr httr2 igraph InteractionSet interp IRanges isoband jpeg jquerylib jsonlite KEGGREST knitr labeling lambda.r lattice latticeExtra lazyeval lifecycle lobstr magrittr MASS Matrix MatrixGenerics matrixStats memoise mime nnet openssl pillar pkgconfig png prettyunits progress ProtGenerics purrr R6 rappdirs RColorBrewer Rcpp RcppEigen RCurl restfulr Rhtslib rjson rlang rmarkdown rpart Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors S7 sass scales Seqinfo snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex UCSC.utils utf8 VariantAnnotation vctrs viridisLite withr xfun XML xml2 XVector yaml

Introduction to CAGEfightR

Rendered fromIntroduction_to_CAGEfightR.Rmdusingknitr::rmarkdown

Last update: 2020-04-10
Started: 2018-01-17

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

Package: CAGEfightR 1.33.0

CAGEfightR: Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor

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