Package: BadRegionFinder 1.40.0

Sarah Sandmann

BadRegionFinder: BadRegionFinder: an R/Bioconductor package for identifying regions with bad coverage

BadRegionFinder is a package for identifying regions with a bad, acceptable and good coverage in sequence alignment data available as bam files. The whole genome may be considered as well as a set of target regions. Various visual and textual types of output are available.

Authors:Sarah Sandmann

BadRegionFinder_1.40.0.tar.gz
BadRegionFinder_1.40.0.zip(r-4.7)BadRegionFinder_1.40.0.zip(r-4.6)BadRegionFinder_1.40.0.zip(r-4.5)
BadRegionFinder_1.40.0.tgz(r-4.6-any)BadRegionFinder_1.40.0.tgz(r-4.5-any)
BadRegionFinder_1.40.0.tar.gz(r-4.7-any)BadRegionFinder_1.40.0.tar.gz(r-4.6-any)
BadRegionFinder_1.40.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
BadRegionFinder/json (API)
NEWS

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

On BioConductor:BadRegionFinder-1.41.0(bioc 3.24)BadRegionFinder-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.

coveragesequencingalignmentwholegenomeclassification

2.30 score 3 scripts 450 downloads 10 exports 89 dependencies

Last updated from:9c97404d87 (on RELEASE_3_23). Checks:9 ERROR, 1 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksERROR267
linux-devel-x86_64ERROR435
source / vignettesERROR386
linux-release-x86_64ERROR433
macos-release-arm64ERROR275
macos-oldrel-arm64ERROR267
windows-develERROR395
windows-releaseERROR304
windows-oldrelERROR327
wasm-releaseOK212

Exports:determineCoveragedetermineCoverageQualitydetermineQuantilesdetermineRegionsOfInterestplotDetailedplotSummaryplotSummaryGenesreportBadRegionsDetailedreportBadRegionsGenesreportBadRegionsSummary

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobBSgenomecachemcigarilloclicodetoolscpp11crayoncurlDBIdbplyrDelayedArraydplyrfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicFeaturesGenomicRangesgluehmshttrhttr2IRangesjsonliteKEGGRESTlambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigpngprettyunitsprogresspurrrR6rappdirsRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsSeqinfosnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectutf8VariantAnnotationvctrswithrXMLxml2XVectoryaml

Readme and manuals

Help Manual

Help pageTopics
BadRegionFinder: an R/Bioconductor package for identifying regions with bad coverageBadRegionFinder-package Bad Coverage BadRegionFinder Coverage Classifier
Determines the coverage (recommended for whole-genome analyses)determineCoverage
Classifies the determined coveragedetermine Coverage Quality determineCoverageQuality
Determines basewise user-defined quantilesdetermine Quantiles determineQuantiles
Determines the regions of interestdetermine Regions Of Interest determineRegionsOfInterest
Plots a more detailed overview of the coverage qualityplot Detailed plotDetailed
Plots a summary of the coverage qualityplot Summary plotSummary
Plots a summary of the coverage quality concerning the genes onlyplot Summary Genes plotSummaryGenes
Gives a detailed report on the coverage qualityreport Bad Regions Detailed reportBadRegionsDetailed
Sums up the coverage quality on a gene basisreport Bad Regions Genes reportBadRegionsGenes
Sums up the coverage qualityreport Bad Regions Summary reportBadRegionsSummary