Package: proActiv 1.15.0

Joseph Lee

proActiv: Estimate Promoter Activity from RNA-Seq data

Most human genes have multiple promoters that control the expression of different isoforms. The use of these alternative promoters enables the regulation of isoform expression pre-transcriptionally. Alternative promoters have been found to be important in a wide number of cell types and diseases. proActiv is an R package that enables the analysis of promoters from RNA-seq data. proActiv uses aligned reads as input, and generates counts and normalized promoter activity estimates for each annotated promoter. In particular, proActiv accepts junction files from TopHat2 or STAR or BAM files as inputs. These estimates can then be used to identify which promoter is active, which promoter is inactive, and which promoters change their activity across conditions. proActiv also allows visualization of promoter activity across conditions.

Authors:Deniz Demircioglu [aut], Jonathan Göke [aut], Joseph Lee [cre]

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proActiv.pdf |proActiv.html✨
proActiv/json (API)
NEWS

# Install 'proActiv' in R:
install.packages('proActiv', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/goekelab/proactiv/issues

Datasets:

On BioConductor:proActiv-1.15.0(bioc 3.20)proActiv-1.14.0(bioc 3.19)

bioconductor-package

26 exports 1.00 score 115 dependencies 1 mentions

Last updated 2 months agofrom:6a63792fed

Exports:%>%arrangeas_tibbleassaysboxplotPromoterscolDatafiltergetAlternativePromotersgroup_byintegrateProactivintronRangesintronRanges<-loadDbmutatenplotHeatmapplotPCApreparePromoterAnnotationproActivPromoterAnnotationpromoterCoordinatespromoterCoordinates<-promoterIdMappingpromoterIdMapping<-rowDatarownames_to_column

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobcachemcaToolsclicodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArrayDESeq2digestdplyrfansifarverfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegplotsgtablegtoolshmshttrhttr2IRangesisobandjsonliteKEGGRESTKernSmoothlabelinglambda.rlatticelifecyclelocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrpngprettyunitsprogresspurrrR6rappdirsRColorBrewerRcppRcppArmadilloRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsscalessnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttxdbmakerUCSC.utilsutf8vctrsviridisLitewithrXMLxml2XVectoryamlzlibbioc

Identifying Active and Alternative Promoters from RNA-Seq data with proActiv

Joseph Lee, Deniz Demircioğlu, Jonathan Göke

Rendered fromproActiv.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2021-05-25
Started: 2020-08-04

Readme and manuals

Help Manual

Help pageTopics
Visualizes promoter activity and gene expression with boxplotsboxplotPromoters
Calculate the total number of junction reads overlapping with the introns of each promoter for the input junction filecalculateJunctionReadCounts
Calculate the promoter read counts using junction read counts approach for all the input junction filescalculatePromoterReadCounts
Prepare the absolute promoter activity table including the promoter and gene idsgetAbsolutePromoterActivity
Identifies alternative promoters.getAlternativePromoters
Prepare the gene expression table including the gene idsgetGeneExpression
Prepare the relative promoter activity table including the promoter and gene idsgetRelativePromoterActivity
Integrate multiple proActiv runsintegrateProactiv
Normalize promoter read counts using DESeq2normalizePromoterReadCounts
Visualizes heatmap of features for samplesplotHeatmap
Performs principal component analysisplotPCA
Prepares promoter annotation from a gtf or txdbpreparePromoterAnnotation
Estimates promoter counts and activity in a single commandproActiv
S4 class for promoter annotation data for a specific annotation version'intronRanges<-',PromoterAnnotation-method 'promoterCoordinates<-',PromoterAnnotation-method 'promoterIdMapping<-',PromoterAnnotation-method intronRanges intronRanges,PromoterAnnotation-method intronRanges<- intronRanges<-,PromoterAnnotation-method PromoterAnnotation PromoterAnnotation-class promoterCoordinates promoterCoordinates,PromoterAnnotation-method promoterCoordinates<- promoterCoordinates<-,PromoterAnnotation-method promoterIdMapping promoterIdMapping,PromoterAnnotation-method promoterIdMapping<- promoterIdMapping<-,PromoterAnnotation-method
Promoter annotation for Gencode.v34 (subset)promoterAnnotation.gencode.v34.subset