Package: BasicSTARRseq 1.41.0

Annika Buerger

BasicSTARRseq: Basic peak calling on STARR-seq data

Basic peak calling on STARR-seq data based on a method introduced in "Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq" Arnold et al. Science. 2013 Mar 1;339(6123):1074-7. doi: 10.1126/science. 1232542. Epub 2013 Jan 17.

Authors:Annika Buerger

BasicSTARRseq_1.41.0.tar.gz
BasicSTARRseq_1.41.0.zip(r-4.7)BasicSTARRseq_1.41.0.zip(r-4.6)BasicSTARRseq_1.41.0.zip(r-4.5)
BasicSTARRseq_1.41.0.tgz(r-4.6-any)BasicSTARRseq_1.41.0.tgz(r-4.5-any)
BasicSTARRseq_1.41.0.tar.gz(r-4.7-any)BasicSTARRseq_1.41.0.tar.gz(r-4.6-any)
BasicSTARRseq_1.41.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
BasicSTARRseq/json (API)

# Install 'BasicSTARRseq' in R:

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

On BioConductor:BasicSTARRseq-1.41.0(bioc 3.24)BasicSTARRseq-1.40.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

peakdetection generegulation functionalprediction functionalgenomics coverage

3.48 score 3 scripts 1 mentions 6 exports 33 dependencies

Last updated from:3d6b5dfc97. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	171
linux-devel-x86_64	NOTE	286
source / vignettes	OK	285
linux-release-x86_64	NOTE	264
macos-release-arm64	NOTE	166
macos-oldrel-arm64	NOTE	213
windows-devel	NOTE	203
windows-release	NOTE	223
windows-oldrel	NOTE	223
wasm-release	OK	120

Exports:control control<-getPeaks sample sample<-STARRseqData

Dependencies:abind BH Biobase BiocGenerics BiocParallel Biostrings bitops cigarillo codetools cpp11 crayon DelayedArray formatR futile.logger futile.options generics GenomicAlignments GenomicRanges IRanges lambda.r lattice Matrix MatrixGenerics matrixStats Rhtslib Rsamtools S4Arrays S4Vectors Seqinfo snow SparseArray SummarizedExperiment XVector

A R/Bioconductor package for basic peak calling on STARR-seq data

Rendered fromBasicSTARRseq.rnwusingutils::Sweave

Last update: 2016-02-09
Started: 2016-02-09

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Peak calling on STARR-seq data	getPeaks getPeaks,STARRseqData-method
Class '"STARRseqData"'	control control,STARRseqData-method control<- control<-,STARRseqData,GRanges-method sample sample,STARRseqData-method sample<- sample<-,STARRseqData,GRanges-method STARRseqData STARRseqData,character,character,logical-method STARRseqData,GRanges,GRanges,ANY-method STARRseqData,GRanges,GRanges-method STARRseqData-class