Package: proActiv 1.23.0

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]

proActiv_1.23.0.tar.gz
proActiv_1.23.0.zip(r-4.7)proActiv_1.23.0.zip(r-4.6)proActiv_1.23.0.zip(r-4.5)
proActiv_1.23.0.tgz(r-4.6-any)proActiv_1.23.0.tgz(r-4.5-any)
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proActiv_1.23.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
proActiv/json (API)

# Install 'proActiv' in R:

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

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

Datasets:

promoterAnnotation.gencode.v34.subset - Promoter annotation for Gencode.v34

On BioConductor:proActiv-1.23.0(bioc 3.24)proActiv-1.22.0(bioc 3.23)

rnaseq geneexpression transcription alternativesplicing generegulation differentialsplicing functionalgenomics epigenetics transcriptomics preprocessing alternative-promoters genomics promoter-activity promoter-annotation rna-seq-data

7.54 score 59 stars 59 scripts 1 mentions 26 exports 109 dependencies

Last updated from:337a775e0d. Checks:1 FAILURE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	FAILURE	1696
linux-devel-x86_64	OK	440
source / vignettes	OK	324
linux-release-x86_64	OK	462
macos-release-arm64	OK	382
macos-oldrel-arm64	OK	313
windows-devel	OK	435
windows-release	OK	389
windows-oldrel	OK	394
wasm-release	OK	162

Exports:%>%arrange as_tibble assays boxplotPromoters colData filter getAlternativePromoters group_by integrateProactiv intronRanges intronRanges<-loadDb mutate n plotHeatmap plotPCA preparePromoterAnnotation proActiv PromoterAnnotation promoterCoordinates promoterCoordinates<-promoterIdMapping promoterIdMapping<-rowData rownames_to_column

Dependencies:abind AnnotationDbi askpass BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings bit bit64 bitops blob cachem caTools cigarillo cli codetools cpp11 crayon curl data.table DBI dbplyr DelayedArray DESeq2 dplyr farver fastmap filelock formatR futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gplots gtable gtools hms httr httr2 IRanges isoband jsonlite KEGGREST KernSmooth labeling lambda.r lattice lifecycle locfit magrittr Matrix MatrixGenerics matrixStats memoise mime openssl pillar pkgconfig png prettyunits progress purrr R6 rappdirs RColorBrewer Rcpp RcppArmadillo RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors S7 scales Seqinfo snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect txdbmaker UCSC.utils utf8 vctrs viridisLite withr XML xml2 XVector yaml

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

Rendered fromproActiv.Rmdusingknitr::rmarkdown

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

Help page	Topics
Visualizes promoter activity and gene expression with boxplots	boxplotPromoters
Calculate the total number of junction reads overlapping with the introns of each promoter for the input junction file	calculateJunctionReadCounts
Calculate the promoter read counts using junction read counts approach for all the input junction files	calculatePromoterReadCounts
Prepare the absolute promoter activity table including the promoter and gene ids	getAbsolutePromoterActivity
Identifies alternative promoters.	getAlternativePromoters
Prepare the gene expression table including the gene ids	getGeneExpression
Prepare the relative promoter activity table including the promoter and gene ids	getRelativePromoterActivity
Integrate multiple proActiv runs	integrateProactiv
Normalize promoter read counts using DESeq2	normalizePromoterReadCounts
Visualizes heatmap of features for samples	plotHeatmap
Performs principal component analysis	plotPCA
Prepares promoter annotation from a gtf or txdb	preparePromoterAnnotation
Estimates promoter counts and activity in a single command	proActiv
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

Package: proActiv 1.23.0

proActiv: Estimate Promoter Activity from RNA-Seq data

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