Package: Rhisat2 1.23.0

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_1.23.0.tar.gz
Rhisat2_1.23.0.zip(r-4.5)Rhisat2_1.23.0.zip(r-4.4)
Rhisat2_1.23.0.tgz(r-4.4-x86_64)Rhisat2_1.23.0.tgz(r-4.4-arm64)
Rhisat2_1.23.0.tar.gz(r-4.5-noble)Rhisat2_1.23.0.tar.gz(r-4.4-noble)
Rhisat2.pdf |Rhisat2.html✨
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:Rhisat2-1.23.0(bioc 3.21)Rhisat2-1.22.0(bioc 3.20)

alignment sequencing splicedalignment cpp

5.95 score 3 stars 1 packages 7 scripts 482 downloads 6 exports 96 dependencies

Last updated 15 hours agofrom:7cc7c6882a. Checks:OK: 1 WARNING: 5. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 22 2024
R-4.5-win-x86_64	WARNING	Dec 03 2024
R-4.5-linux-x86_64	WARNING	Dec 22 2024
R-4.4-win-x86_64	WARNING	Dec 03 2024
R-4.4-mac-x86_64	WARNING	Dec 22 2024
R-4.4-mac-aarch64	WARNING	Dec 22 2024

Exports:extract_splice_sites hisat2 hisat2_build hisat2_build_usage hisat2_usage hisat2_version

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

Aligning reads with Rhisat2

Charlotte Soneson

Rendered fromRhisat2.Rmdusingknitr::rmarkdownon Dec 22 2024.

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