Package: breakpointR 1.31.0

David Porubsky

breakpointR: Find breakpoints in Strand-seq data

This package implements functions for finding breakpoints, plotting and export of Strand-seq data.

Authors:David Porubsky, Ashley Sanders, Aaron Taudt

breakpointR_1.31.0.tar.gz
breakpointR_1.31.0.zip(r-4.7)breakpointR_1.31.0.zip(r-4.6)breakpointR_1.31.0.zip(r-4.5)
breakpointR_1.31.0.tgz(r-4.6-any)breakpointR_1.31.0.tgz(r-4.5-any)
breakpointR_1.31.0.tar.gz(r-4.7-any)breakpointR_1.31.0.tar.gz(r-4.6-any)
breakpointR_1.31.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
breakpointR/json (API)

# Install 'breakpointR' in R:

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

Bug tracker:https://github.com/daewoooo/breakpointr/issues

On BioConductor:breakpointR-1.31.0(bioc 3.24)breakpointR-1.30.0(bioc 3.23)

software sequencing dnaseq singlecell coverage

5.83 score 9 stars 15 scripts 19 exports 64 dependencies

Last updated from:098c4f2f46. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	199
linux-devel-x86_64	NOTE	406
source / vignettes	OK	294
linux-release-x86_64	NOTE	388
macos-release-arm64	NOTE	178
macos-oldrel-arm64	NOTE	169
windows-devel	NOTE	301
windows-release	NOTE	256
windows-oldrel	NOTE	271
wasm-release	OK	152

Exports:breakpointr breakpointr2UCSC breakSeekr deltaWCalculator exportRegions genotype.binom genotype.fisher GenotypeBreaks hotspotter loadFromFiles plotBreakpoints plotBreakpointsPerChr plotHeatmap ranges2UCSC readBamFileAsGRanges removeReadPileupSpikes runBreakpointr summarizeBreaks synchronizeReadDir

Dependencies:abind askpass BH Biobase BiocGenerics BiocParallel Biostrings bitops breakpointRdata cigarillo cli codetools cowplot cpp11 crayon curl DelayedArray doParallel farver foreach formatR futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 glue gtable gtools httr IRanges isoband iterators jsonlite labeling lambda.r lattice lifecycle Matrix MatrixGenerics matrixStats mime openssl R6 RColorBrewer Rhtslib rlang Rsamtools S4Arrays S4Vectors S7 scales Seqinfo snow SparseArray SummarizedExperiment sys UCSC.utils vctrs viridisLite withr XVector

How to use breakpointR

1 Introduction | 2 Quickstart | 3 Recommended settings | 4 Session Info

Rendered frombreakpointR.Rnwusingknitr::knitr

Last update: 2019-08-04
Started: 2017-03-31

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Breakpoint detection in Strand-Seq data	breakpointR-package breakpointR
BreakPoint object	BreakPoint
Main function for the 'breakpointR' package	breakpointr
Export UCSC browser formated files	breakpointr2UCSC
Find breakpoints from deltaWs	breakSeekr
Collapse consecutive bins with the same ID value	collapseBins
Estimate confidence intervals for breakpoints	confidenceInterval
Estimate confidence intervals for breakpoints	confidenceInterval.binomial
Create composite Strand-seq file	createCompositeFile
Calculate deltaWs	deltaWCalculator
Calculate deltaWs using various window sizes	deltaWCalculatorVariousWindows
Function to print WC regions after breakpointR analysis	exportRegions
Assign states to any given region using binomial test.	genotype.binom
Assign states to any given region using Fisher Exact Test.	genotype.fisher
Set of functions to genotype regions in between localized breakpoints	GenotypeBreaks genotyping
Find hotspots of genomic events	hotspotter
Insert chromosome for in case it's missing	insertchr
Load 'breakpointR' objects from file	loadFromFiles
Plotting genome-wide ideograms 'breakpointR'	plotBreakpoints
Plotting chromosome specific ideograms 'breakpointR'	plotBreakpointsPerChr
Genome wide heatmap of template inheritance states	plotHeatmap
Generates a bedfile from an input GRanges file	ranges2UCSC
Import BAM file into GRanges	readBamFileAsGRanges
Read breakpointR configuration file	readConfig
Process double SCE chromosomes: with internal WC region.	removeDoubleSCEs
Remove large spikes in short reads coverage	removeReadPileupSpikes
Find breakpoints in Strand-seq data	runBreakpointr
Compile breakpoint summary table	summarizeBreaks
Synchronize Strand-seq read directionality	synchronizeReadDir
Transform genomic coordinates	transCoord
Write breakpointR configuration file	writeConfig