Package: BadRegionFinder 1.35.0

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_1.35.0.tar.gz
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BadRegionFinder_1.35.0.tgz(r-4.4-any)BadRegionFinder_1.35.0.tgz(r-4.3-any)
BadRegionFinder_1.35.0.tar.gz(r-4.5-noble)BadRegionFinder_1.35.0.tar.gz(r-4.4-noble)
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BadRegionFinder.pdf |BadRegionFinder.html✨
BadRegionFinder/json (API)
NEWS

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

Peer review:

On BioConductor:BadRegionFinder-1.35.0(bioc 3.21)BadRegionFinder-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.

coveragesequencingalignmentwholegenomeclassification

3.30 score 1 scripts 266 downloads 10 exports 94 dependencies

Last updated 23 days agofrom:7025a464be. Checks:OK: 1 WARNING: 4 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 19 2024
R-4.5-winWARNINGNov 19 2024
R-4.5-linuxWARNINGNov 19 2024
R-4.4-winWARNINGNov 19 2024
R-4.4-macNOTENov 19 2024
R-4.3-winWARNINGNov 19 2024
R-4.3-macNOTENov 19 2024

Exports:determineCoveragedetermineCoverageQualitydetermineQuantilesdetermineRegionsOfInterestplotDetailedplotSummaryplotSummaryGenesreportBadRegionsDetailedreportBadRegionsGenesreportBadRegionsSummary

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobBSgenomecachemclicodetoolscpp11crayoncurlDBIdbplyrDelayedArraydigestdplyrfansifastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesgluehmshttrhttr2IRangesjsonliteKEGGRESTlambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigplogrpngprettyunitsprogresspurrrR6rappdirsRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorssnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8VariantAnnotationvctrswithrXMLxml2XVectoryamlzlibbioc

Using BadRegionFinder

Rendered fromBadRegionFinder.Rnwusingutils::Sweaveon Nov 19 2024.

Last update: 2018-08-28
Started: 2016-03-29

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