Rhtslib
Rhtslib provides HTSlib version 1.1 as an R-accessible C library to enable programmatic handling of high-throughput sequencing data for genomic analyses such as variant calling, sequence alignment, and transcriptome analysis within the Bioconductor ecosystem.
Key Features:
- Integration with Bioconductor: Distributed as a Bioconductor package that exposes HTSlib functionality to the R environment.
- Bundled HTSlib C library (v1.1): Includes HTSlib v1.1 compiled for use from R to provide native HTSlib routines.
- Developer-oriented API: Provides interfaces for R package developers to integrate HTSlib capabilities into custom bioinformatics applications.
Scientific Applications:
- Genomics and Molecular Biology: Enables analysis of large-scale sequencing data supporting variant calling, sequence alignment, and transcriptome analysis.
Methodology:
R package that supplies R bindings to the HTSlib v1.1 C library, enabling R code to call HTSlib routines for processing high-throughput sequencing data.
Topics
Collections
Details
- License:
- GPL-2.0
- Tool Type:
- command-line tool, library
- Operating Systems:
- Linux, Windows, Mac
- Programming Languages:
- R
- Added:
- 1/17/2017
- Last Updated:
- 11/25/2024
Operations
Publications
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M. Orchestrating high-throughput genomic analysis with Bioconductor. Nature Methods. 2015;12(2):115-121. doi:10.1038/nmeth.3252. PMID:25633503. PMCID:PMC4509590.