Package: Rhisat2 1.29.1

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_1.29.1.tar.gz
Rhisat2_1.29.1.zip(r-4.7-x86_64)Rhisat2_1.29.1.zip(r-4.7-arm64)Rhisat2_1.29.1.zip(r-4.6-x86_64)Rhisat2_1.29.1.zip(r-4.6-arm64)Rhisat2_1.29.1.zip(r-4.5-x86_64)
Rhisat2_1.29.1.tgz(r-4.6-x86_64)Rhisat2_1.29.1.tgz(r-4.6-arm64)Rhisat2_1.29.1.tgz(r-4.5-x86_64)Rhisat2_1.29.1.tgz(r-4.5-arm64)
Rhisat2_1.29.1.tar.gz(r-4.7-arm64)Rhisat2_1.29.1.tar.gz(r-4.7-x86_64)Rhisat2_1.29.1.tar.gz(r-4.6-arm64)Rhisat2_1.29.1.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Rhisat2/json (API)

# 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:Rhisat2-1.29.1(bioc 3.24)Rhisat2-1.28.1(bioc 3.23)

alignment sequencing splicedalignment cpp

5.87 score 3 stars 1 packages 11 scripts 608 downloads 6 exports 94 dependencies

Last updated from:05a1f28550. Checks:14 WARNING, 1 OK, 1 FAIL. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	232
linux-devel-arm64	WARNING	366
linux-devel-x86_64	WARNING	473
source / vignettes	OK	520
linux-release-arm64	WARNING	411
linux-release-x86_64	WARNING	496
macos-release-arm64	WARNING	303
macos-release-x86_64	WARNING	587
macos-oldrel-arm64	WARNING	278
macos-oldrel-x86_64	WARNING	744
windows-devel-arm64	WARNING	476
windows-devel-x86_64	WARNING	493
windows-release-arm64	WARNING	465
windows-release-x86_64	WARNING	485
windows-oldrel-x86_64	WARNING	395
wasm-release	FAIL	129

Exports:extract_splice_sites hisat2 hisat2_build hisat2_build_usage hisat2_usage hisat2_version

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

Aligning reads with Rhisat2

Rendered fromRhisat2.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Extract splice sites from annotation	extract_splice_sites
Align reads with HISAT2	hisat2
Generate HISAT2 index	hisat2_build
Print usage of hisat2-build	hisat2_build_usage
Print usage of hisat2	hisat2_usage
Print HISAT2 version	hisat2_version