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BSgenome.Ggallus.UCSC.galGal3.masked

This is the development version of BSgenome.Ggallus.UCSC.galGal3.masked; for the stable release version, see BSgenome.Ggallus.UCSC.galGal3.masked.

All versions 3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14

Full masked genome sequences for Gallus gallus (UCSC version galGal3)


Bioconductor version: Development (3.24)

Full genome sequences for Gallus gallus (Chicken) as provided by UCSC (galGal3, May 2006) and stored in Biostrings objects. The sequences are the same as in BSgenome.Ggallus.UCSC.galGal3, 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.

Author: The Bioconductor Dev Team

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

Citation (from within R, enter citation("BSgenome.Ggallus.UCSC.galGal3.masked")):

The Bioconductor Dev Team. BSgenome.Ggallus.UCSC.galGal3.masked: Full masked genome sequences for Gallus gallus (UCSC version galGal3). doi:10.18129/B9.bioc.BSgenome.Ggallus.UCSC.galGal3.masked, R package version 1.3.99, https://bioconductor.org/packages/BSgenome.Ggallus.UCSC.galGal3.masked.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

BiocManager::install("BSgenome.Ggallus.UCSC.galGal3.masked")

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

Documentation

No vignettes available
Reference ManualPDF
Need some help? Ask on the Bioconductor Support site!

Details

biocViews AnnotationData, BSgenome, Gallus_gallus, Genetics
Version1.3.99
In Bioconductor sinceBioC 2.14 (R-3.1) (12.5 years)
License Artistic-2.0
Depends BSgenome (>= 1.31.8), BSgenome.Ggallus.UCSC.galGal3
Imports BSgenome, BSgenome.Ggallus.UCSC.galGal3
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Follow Installation instructions to use this package in your R session.

Source Package BSgenome.Ggallus.UCSC.galGal3.masked_1.3.99.tar.gz
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)
macOS Binary (sonoma-arm64)
Package Short Url https://bioconductor.org/packages/BSgenome.Ggallus.UCSC.galGal3.masked/
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