Name Mode Size
R 040000
data 040000
inst 040000
man 040000
tests 040000
vignettes 040000
DESCRIPTION 100644 1 kb
NAMESPACE 100644 1 kb 100644 2 kb
# packFinder <img src="inst/packFinder_hex.png" align="right" height="174" width="150" /> A package for the *de novo* discovery of Pack-TYPE transposons. Transposons are detected in DNA sequences based on conserved terminal inverted repeat sequences and presence of terminal site duplications. `packFinder` allows users to search a given Genome for Pack-TYPE transposons with minimal input and setup. For a more in-depth explanation, see our [paper in PLOS Genetics]( ## Installation `packFinder` is available from the [Bioconductor project]( With R >=4.0.0 installed, the following code can be used to install the package: ``` if (!require("BiocManager")) install.packages("BiocManager") BiocManager::install("packFinder") ``` In order to use the functions `packClust` and `packAlign`, the VSEARCH command line tool must be installed. For Linux and MacOS systems, correct installation of VSEARCH should allow users to use all functions within `packFinder`; for windows users, the absolute path to the VSEARCH executable file must be specified when calling `packFinder` clustering and alignment functions. See the vignette, documentation or the [VSEARCH github]( for further information. Additionally, utilites are provided with the package for the functional annotation of internal transposon sequences using BLAST+; this application can be installed from [NCBI]( ## Using packFinder The `packFinder` vignette includes a full walkthrough of the package. To get started quickly, it is easiest to download a genome of interest using the `biomartr` package and follow the steps outlined in [the vignette]( ## Citation If you use `packFinder` in your work, please cite the following publication: > Gisby, J. S. & Catoni, M. (2022) [The widespread nature of Pack-TYPE transposons reveals their importance for plant genome evolution.]( *PLOS Genetics* 18(2): e1010078. >