Package: BasicSTARRseq 1.35.0

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_1.35.0.tar.gz
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BasicSTARRseq_1.35.0.tgz(r-4.4-any)BasicSTARRseq_1.35.0.tgz(r-4.3-any)
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BasicSTARRseq.pdf |BasicSTARRseq.html✨
BasicSTARRseq/json (API)
NEWS

# Install 'BasicSTARRseq' in R:

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

On BioConductor:BasicSTARRseq-1.35.0(bioc 3.21)BasicSTARRseq-1.34.0(bioc 3.20)

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

3.30 score 1 scripts 277 downloads 1 mentions 6 exports 42 dependencies

Last updated 2 months agofrom:2f45ad6b5d. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 21 2024
R-4.5-win	NOTE	Nov 21 2024
R-4.5-linux	NOTE	Dec 21 2024
R-4.4-win	NOTE	Nov 21 2024
R-4.4-mac	NOTE	Dec 21 2024
R-4.3-win	NOTE	Nov 21 2024
R-4.3-mac	NOTE	Dec 21 2024

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

Dependencies:abind askpass BH Biobase BiocGenerics BiocParallel Biostrings bitops codetools cpp11 crayon curl DelayedArray formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicRanges httr IRanges jsonlite lambda.r lattice Matrix MatrixGenerics matrixStats mime openssl R6 Rhtslib Rsamtools S4Arrays S4Vectors snow SparseArray SummarizedExperiment sys UCSC.utils XVector

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

Rendered fromBasicSTARRseq.rnwusingutils::Sweaveon Dec 21 2024.

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