Package: Rhisat2 1.29.0

Charlotte Soneson

Rhisat2: R Wrapper for HISAT2 Aligner

An R interface to the HISAT2 spliced short-read aligner by Kim et al. (2015). The package contains wrapper functions to create a genome index and to perform the read alignment to the generated index.

Authors:Charlotte Soneson [aut, cre]

Rhisat2_1.29.0.tar.gz
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Rhisat2_1.29.0.tgz(r-4.6-x86_64)Rhisat2_1.29.0.tgz(r-4.6-arm64)Rhisat2_1.29.0.tgz(r-4.5-x86_64)Rhisat2_1.29.0.tgz(r-4.5-arm64)
Rhisat2_1.29.0.tar.gz(r-4.7-arm64)Rhisat2_1.29.0.tar.gz(r-4.7-x86_64)Rhisat2_1.29.0.tar.gz(r-4.6-arm64)Rhisat2_1.29.0.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
card.svg |card.png
Rhisat2/json (API)
NEWS

# Install 'Rhisat2' in R:
install.packages('Rhisat2', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/fmicompbio/rhisat2/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On BioConductor:Rhisat2-1.29.0(bioc 3.24)Rhisat2-1.28.0(bioc 3.23)

alignmentsequencingsplicedalignmentcpp

5.56 score 3 stars 1 packages 7 scripts 565 downloads 6 exports 94 dependencies

Last updated from:7fe4d07421. Checks:1 NOTE, 11 WARNING, 1 OK, 1 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE273
linux-devel-arm64WARNING427
linux-devel-x86_64WARNING488
source / vignettesOK511
linux-release-arm64WARNING432
linux-release-x86_64WARNING568
macos-release-arm64WARNING242
macos-release-x86_64WARNING838
macos-oldrel-arm64WARNING374
macos-oldrel-x86_64WARNING606
windows-develWARNING582
windows-releaseWARNING542
windows-oldrelWARNING497
wasm-releaseFAIL158

Exports:extract_splice_siteshisat2hisat2_buildhisat2_build_usagehisat2_usagehisat2_version

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobcachemcigarilloclicodetoolscpp11crayoncurlDBIdbplyrDelayedArraydplyrfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesgluehmshttrhttr2igraphIRangesjsonliteKEGGRESTlambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigpngprettyunitsprogresspurrrR6rappdirsRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerRUnitS4ArraysS4VectorsSeqinfoSGSeqsnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttxdbmakerUCSC.utilsutf8vctrswithrXMLxml2XVectoryaml

Aligning reads with Rhisat2

Charlotte Soneson

Rendered fromRhisat2.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2019-02-01
Started: 2018-10-17