README.md

In bioinfo16/IRFinder: Vector integrated region analysis package (IRFinder)

IRFinder

Vector integrated region analysis tool (temp)

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 (Recommanded, automatically install required packages) devtools::install_github("bioinfo16/IRFinder")

• 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 IRFinder. R CMD INSTALL [PACKAGE_DOWNLOAD_PATH]

• Package information If you want to use IRFinder, 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)
  • grDevices (>=3.5.3)
  • karyoploteR (>=1.6.3)
  • plyr (>=1.8.4)
  • regioneR (>=1.12.0)
  • stats (>=3.5.3)
  • stringr (>=1.3.1)
  • utils (>=3.5.3)

We tested the package in this session environment. ``` R version 3.5.3 (2019-03-11) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale: [1] LC_COLLATE=Korean_Korea.949 LC_CTYPE=Korean_Korea.949 LC_MONETARY=Korean_Korea.949 LC_NUMERIC=C [5] LC_TIME=Korean_Korea.949

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

other attached packages: [1] karyoploteR_1.6.3 regioneR_1.12.0 BSgenome_1.48.0 rtracklayer_1.40.6 Biostrings_2.48.0 [6] XVector_0.20.0 memoise_1.1.0 quantreg_5.42.1 SparseM_1.77 plyr_1.8.4 [11] stringr_1.4.0 GenomicRanges_1.34.0 GenomeInfoDb_1.18.2 IRanges_2.16.0 S4Vectors_0.20.1 [16] BiocGenerics_0.28.0

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

bioinfo16/IRFinder documentation built on Aug. 19, 2019, 10:37 a.m.