packFinder
This is the development version of packFinder; for the stable release version, see packFinder.
de novo Annotation of Pack-TYPE Transposable Elements
Bioconductor version: Development (3.24)
Algorithm and tools for in silico pack-TYPE transposon discovery. Filters a given genome for properties unique to DNA transposons and provides tools for the investigation of returned matches. Sequences are input in DNAString format, and ranges are returned as a dataframe (in the format returned by as.dataframe(GRanges)).
Author: Jack Gisby [aut, cre]
, Marco Catoni [aut]
Maintainer: Jack Gisby <jackgisby at gmail.com>
citation("packFinder")):
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 (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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("packFinder")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("packFinder")| packFinder | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Annotation, Genetics, SequenceMatching, Software |
| Version | 1.25.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (6.5 years) |
| License | GPL-2 |
| Depends | R (>= 4.1.0) |
| Imports | Biostrings, GenomicRanges, kmer, ape, methods, IRanges, S4Vectors |
| System Requirements | |
| URL | https://github.com/jackgisby/packFinder |
| Bug Reports | https://github.com/jackgisby/packFinder/issues |
See More
| Suggests | biomartr, knitr, rmarkdown, testthat, dendextend, biocViews, BiocCheck, BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | packFinder_1.25.0.tar.gz |
| Windows Binary (x86_64) | packFinder_1.25.0.zip |
| macOS Binary (big-sur-x86_64) | packFinder_1.25.0.tgz |
| macOS Binary (sonoma-arm64) | packFinder_1.25.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/packFinder |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/packFinder |
| Bioc Package Browser | https://code.bioconductor.org/browse/packFinder/ |
| Package Short Url | https://bioconductor.org/packages/packFinder/ |
| Package Downloads Report | Download Stats |