BSgenome.Hsapiens.UCSC.hg38.masked

This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see BSgenome.Hsapiens.UCSC.hg38.masked.

Full masked genomic sequences for Homo sapiens (UCSC version hg38)

DOI: 10.18129/B9.bioc.BSgenome.Hsapiens.UCSC.hg38.masked

Bioconductor version: 3.19

Full genomic sequences for Homo sapiens as provided by UCSC (genome hg38, based on assembly GRCh38.p14 since 2023年01月31日). The sequences are the same as in BSgenome.Hsapiens.UCSC.hg38, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default. The sequences are stored in MaskedDNAString objects.

Author: The Bioconductor Dev Team

Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>

Citation (from within R, enter citation("BSgenome.Hsapiens.UCSC.hg38.masked")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("BSgenome.Hsapiens.UCSC.hg38.masked")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

Reference Manual PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews AnnotationData, BSgenome, Genetics, Homo_sapiens

Version 1.4.5

License Artistic-2.0

Depends R (>= 4.2.0), GenomeInfoDb(>= 1.34.9), BSgenome(>= 1.66.2), BSgenome.Hsapiens.UCSC.hg38

Imports

System Requirements

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Suggests Me BSgenome, podkat, spiky

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Follow Installation instructions to use this package in your R session.

Source Package BSgenome.Hsapiens.UCSC.hg38.masked_1.4.5.tar.gz

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Package Short Url https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38.masked/

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