README.md

In bioinfo16/VVIPS: Viral Vector Integration Position Seeker

VVIPS

Viral Vector Integration Position Seeker

This tool is developed for analysis of viral vector integration site analysis. Researchers who want to use this R package, need to input file acquired by BLAST(NCBI) or BLAT(UCSC). If you have any question about this package, contact to author by this e-mail, [e-mail].

• Install package We recommand the way using devtools package in R. But, you can download this package like zipped file from this repository. Plus, we wiil upload this package in Bioconductor repository. It's in progress.
• Using devtools (Recommended) devtools::install_github("bioinfo16/VVIPS")

• Or, donwload it through the menu releases and enter the following command in the console. But, this way doesn't install package which is needed for running VVIPS. R CMD INSTALL [PACKAGE_DOWNLOAD_PATH]

• Package information If you want to use VVIPS, please install R, version 3.5.3 is recommanded. Plus, users can automatically install these required packages below by devtools.

• Required packages (package version)

  • biomaRt (>=2.38.0)
  • GenomeInfoDb (>=1.18.1)
  • GenomicRanges (>=1.34.0)
  • ggplot2 (>= 3.1.0)
  • grDevices (>=3.5.3)
  • karyoploteR (>=1.6.3)
  • plyr (>=1.8.4)
  • stats (>=3.5.3)
  • stringr (>=1.3.1)
  • utils (>=3.5.3)
  • writexl (>= 1.1)

We tested the package in this session environment. ``` R version 3.5.3 (2019-03-11) Platform: i386-w64-mingw32/i386 (32-bit) Running under: Windows 7 (build 7601) Service Pack 1

Matrix products: default

locale: [1] LC_COLLATE=Korean_Korea.949 LC_CTYPE=Korean_Korea.949 LC_MONETARY=Korean_Korea.949 [4] LC_NUMERIC=C LC_TIME=Korean_Korea.949

attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets methods base

other attached packages: [1] biomaRt_2.38.0 writexl_1.1 plyr_1.8.4 karyoploteR_1.8.8 [5] regioneR_1.14.0 GenomicRanges_1.34.0 GenomeInfoDb_1.18.2 IRanges_2.16.0 [9] S4Vectors_0.20.1 BiocGenerics_0.28.0 ggplot2_3.2.1 stringr_1.4.0

(...skipped...) ```

bioinfo16/VVIPS documentation built on Nov. 4, 2019, 7:20 a.m.