Package: Rhisat2 1.28.0

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_1.28.0.tar.gz
Rhisat2_1.28.0.zip(r-4.7)Rhisat2_1.28.0.zip(r-4.6)Rhisat2_1.28.0.zip(r-4.5)
Rhisat2_1.28.0.tgz(r-4.6-x86_64)Rhisat2_1.28.0.tgz(r-4.6-arm64)Rhisat2_1.28.0.tgz(r-4.5-x86_64)Rhisat2_1.28.0.tgz(r-4.5-arm64)
Rhisat2_1.28.0.tar.gz(r-4.7-arm64)Rhisat2_1.28.0.tar.gz(r-4.7-x86_64)Rhisat2_1.28.0.tar.gz(r-4.6-arm64)Rhisat2_1.28.0.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-release.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 8 scripts 6 exports 93 dependencies

Last updated from:74b81caf0e (on RELEASE_3_23). Checks:1 NOTE, 11 WARNING, 1 OK, 1 FAIL. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksNOTE303
linux-devel-arm64WARNING432
linux-devel-x86_64WARNING521
source / vignettesOK502
linux-release-arm64WARNING425
linux-release-x86_64WARNING562
macos-release-arm64WARNING280
macos-release-x86_64WARNING495
macos-oldrel-arm64WARNING228
macos-oldrel-x86_64WARNING529
windows-develWARNING519
windows-releaseWARNING492
windows-oldrelWARNING542
wasm-releaseFAIL149

Exports:extract_splice_siteshisat2hisat2_buildhisat2_build_usagehisat2_usagehisat2_version

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobcachemcigarilloclicodetoolscpp11crayoncurlDBIdbplyrDelayedArraydplyrfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesgluehmshttrhttr2igraphIRangesjsonliteKEGGRESTlambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigpngprettyunitsprogresspurrrR6rappdirsRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerRUnitS4ArraysS4VectorsSeqinfoSGSeqsnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttxdbmakerUCSC.utilsutf8vctrswithrXMLxml2XVectoryaml

Aligning reads with Rhisat2

Charlotte Soneson

Rendered fromRhisat2.Rmdusingknitr::rmarkdownon Jun 21 2026.

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