Package: HelloRanges 1.39.0
Michael Lawrence
HelloRanges: Introduce *Ranges to bedtools users
Translates bedtools command-line invocations to R code calling functions from the Bioconductor *Ranges infrastructure. This is intended to educate novice Bioconductor users and to compare the syntax and semantics of the two frameworks.
Authors:
HelloRanges_1.39.0.tar.gz
HelloRanges_1.39.0.zip(r-4.7)HelloRanges_1.39.0.zip(r-4.6)HelloRanges_1.39.0.zip(r-4.5)
HelloRanges_1.39.0.tgz(r-4.6-any)HelloRanges_1.39.0.tgz(r-4.5-any)
HelloRanges_1.39.0.tar.gz(r-4.7-any)HelloRanges_1.39.0.tar.gz(r-4.6-any)
HelloRanges_1.39.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
HelloRanges/json (API)
NEWS
| # Install 'HelloRanges' in R: |
| install.packages('HelloRanges', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:HelloRanges-1.39.0(bioc 3.24)HelloRanges-1.38.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
sequencingannotationcoveragegenomeannotationdataimportsequencematchingvariantannotation
Last updated from:d0d14f2ba8. Checks:2 ERROR, 7 WARNING, 1 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 233 | ||
| linux-devel-x86_64 | WARNING | 483 | ||
| source / vignettes | ERROR | 364 | ||
| linux-release-x86_64 | WARNING | 400 | ||
| macos-release-arm64 | WARNING | 291 | ||
| macos-oldrel-arm64 | WARNING | 236 | ||
| windows-devel | WARNING | 356 | ||
| windows-release | WARNING | 337 | ||
| windows-oldrel | WARNING | 331 | ||
| wasm-release | OK | 181 |
Exports:.R_bedtools_disjoinbedtools_closestbedtools_complementbedtools_coveragebedtools_flankbedtools_genomecovbedtools_getfastabedtools_groupbybedtools_intersectbedtools_jaccardbedtools_makewindowsbedtools_mapbedtools_mergebedtools_multiinterbedtools_nucbedtools_shiftbedtools_slopbedtools_subtractbedtools_unionbedgdistmodedo_bedtools_closestdo_bedtools_complementdo_bedtools_coveragedo_bedtools_flankdo_bedtools_genomecovdo_bedtools_getfastado_bedtools_groupbydo_bedtools_intersectdo_bedtools_jaccarddo_bedtools_makewindowsdo_bedtools_mapdo_bedtools_mergedo_bedtools_multiinterdo_bedtools_nucdo_bedtools_shiftdo_bedtools_slopdo_bedtools_subtractdo_bedtools_unionbedgpairR_bedtools_closestR_bedtools_complementR_bedtools_coverageR_bedtools_flankR_bedtools_genomecovR_bedtools_getfastaR_bedtools_groupbyR_bedtools_intersectR_bedtools_jaccardR_bedtools_makewindowsR_bedtools_mapR_bedtools_mergeR_bedtools_multiinterR_bedtools_nucR_bedtools_shiftR_bedtools_slopR_bedtools_subtractR_bedtools_unionbedg
Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemcigarilloclicodetoolscpp11crayoncurlDBIDelayedArraydocoptfastmapformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicFeaturesGenomicRangesgluehttrIRangesjsonliteKEGGRESTlambda.rlatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigpngR6RCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsSeqinfosnowSparseArraySummarizedExperimentsysVariantAnnotationvctrsXMLXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Argument parsing details | argparsing |
| bedtools_closest | bedtools_closest do_bedtools_closest R_bedtools_closest |
| bedtools_complement | bedtools_complement do_bedtools_complement R_bedtools_complement |
| bedtools_coverage | bedtools_coverage do_bedtools_coverage R_bedtools_coverage |
| bedtools_flank | bedtools_flank do_bedtools_flank R_bedtools_flank |
| bedtools_genomecov | bedtools_genomecov do_bedtools_genomecov R_bedtools_genomecov |
| bedtools_getfasta | bedtools_getfasta do_bedtools_getfasta R_bedtools_getfasta |
| bedtools_groupby | bedtools_groupby do_bedtools_groupby R_bedtools_groupby |
| bedtools_intersect | bedtools_intersect do_bedtools_intersect R_bedtools_intersect |
| bedtools_jaccard | bedtools_jaccard do_bedtools_jaccard R_bedtools_jaccard |
| bedtools_makewindows | bedtools_makewindows do_bedtools_makewindows R_bedtools_makewindows |
| bedtools_map | bedtools_map do_bedtools_map R_bedtools_map |
| bedtools_merge | bedtools_merge do_bedtools_merge R_bedtools_merge |
| bedtools_multiinter | bedtools_multiinter do_bedtools_multiinter R_bedtools_multiinter |
| bedtools_nuc | bedtools_nuc do_bedtools_nuc R_bedtools_nuc |
| bedtools_shift | bedtools_shift do_bedtools_shift R_bedtools_shift |
| bedtools_slop | bedtools_slop do_bedtools_slop R_bedtools_slop |
| bedtools_subtract | bedtools_subtract do_bedtools_subtract R_bedtools_subtract |
| bedtools_unionbedg | bedtools_unionbedg do_bedtools_unionbedg R_bedtools_unionbedg |
| Compute the mode of a distribution | distmode distmode,CompressedAtomicList-method distmode,factor-method distmode,SimpleList-method distmode,vector-method |
| Pair up two vectors | pair pair,GAlignments,GenomicRanges-method pair,GenomicRanges,GenomicRanges-method pair,SummarizedExperiment,GenomicRanges-method pair,Vector,Vector-method |
