Package: BadRegionFinder 1.41.0

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_1.41.0.tar.gz
BadRegionFinder_1.41.0.zip(r-4.7)BadRegionFinder_1.41.0.zip(r-4.6)BadRegionFinder_1.41.0.zip(r-4.5)
BadRegionFinder_1.41.0.tgz(r-4.6-any)BadRegionFinder_1.41.0.tgz(r-4.5-any)
BadRegionFinder_1.41.0.tar.gz(r-4.7-any)BadRegionFinder_1.41.0.tar.gz(r-4.6-any)
BadRegionFinder_1.41.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
BadRegionFinder/json (API)

# Install 'BadRegionFinder' in R:

install.packages('BadRegionFinder', repos = c('https://bioc.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.

coverage sequencing alignment wholegenome classification

3.30 score 3 scripts 450 downloads 10 exports 90 dependencies

Last updated from:73aca6b16a. Checks:8 ERROR, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	265
linux-devel-x86_64	ERROR	511
source / vignettes	OK	408
linux-release-x86_64	ERROR	449
macos-release-arm64	ERROR	288
macos-oldrel-arm64	ERROR	318
windows-devel	ERROR	326
windows-release	ERROR	328
windows-oldrel	ERROR	330
wasm-release	OK	215

Exports:determineCoverage determineCoverageQuality determineQuantiles determineRegionsOfInterest plotDetailed plotSummary plotSummaryGenes reportBadRegionsDetailed reportBadRegionsGenes reportBadRegionsSummary

Dependencies:abind AnnotationDbi askpass BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings bit bit64 bitops blob BSgenome cachem cigarillo cli codetools cpp11 crayon curl DBI dbplyr DelayedArray dplyr fastmap filelock formatR futile.logger futile.options generics GenomicAlignments GenomicFeatures GenomicRanges glue hms httr httr2 IRanges jsonlite KEGGREST lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime openssl pillar pkgconfig png prettyunits progress purrr R6 rappdirs RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors Seqinfo snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect utf8 VariantAnnotation vctrs withr XML xml2 XVector yaml

Using BadRegionFinder

Rendered fromBadRegionFinder.Rnwusingutils::Sweave

Last update: 2025-01-26
Started: 2016-03-29

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
BadRegionFinder: an R/Bioconductor package for identifying regions with bad coverage	BadRegionFinder-package Bad Coverage BadRegionFinder Coverage Classifier
Determines the coverage (recommended for whole-genome analyses)	determineCoverage
Classifies the determined coverage	determine Coverage Quality determineCoverageQuality
Determines basewise user-defined quantiles	determine Quantiles determineQuantiles
Determines the regions of interest	determine Regions Of Interest determineRegionsOfInterest
Plots a more detailed overview of the coverage quality	plot Detailed plotDetailed
Plots a summary of the coverage quality	plot Summary plotSummary
Plots a summary of the coverage quality concerning the genes only	plot Summary Genes plotSummaryGenes
Gives a detailed report on the coverage quality	report Bad Regions Detailed reportBadRegionsDetailed
Sums up the coverage quality on a gene basis	report Bad Regions Genes reportBadRegionsGenes
Sums up the coverage quality	report Bad Regions Summary reportBadRegionsSummary