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README.md
[![Release](https://img.shields.io/github/release/bioinfo16/RIPAT.svg)](https://github.com/bioinfo16/RIPAT/releases) [![Downloads](https://img.shields.io/github/downloads/bioinfo16/RIPAT/total?logo=github)](https://github.com/bioinfo16/RIPAT/releases/download/v0.99.0/RIPAT_v0.99.0.tar.gz) [![Issues](https://img.shields.io/github/issues/bioinfo16/RIPAT.svg)](https://github.com/bioinfo16/RIPAT/issues) # RIPAT #### Retroviral Integration Pattern Analysis Tool This tool is developed for viral vector integration pattern analysis. Researchers who want to use this R package, need to input file generated by BLAST(NCBI) or BLAT(UCSC). If you have any question about this package, contact to author by this e-mail, *mjbaek16@korea.ac.kr*. ***** * 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/RIPAT") ``` - 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 __RIPAT__. ``` R CMD INSTALL [PACKAGE_DOWNLOAD_PATH] ``` * Package information If you want to use __RIPAT__, please install **R** (>=4.0) is recommanded. Plus, users can install these required packages (GeonomicRanges, IRanges, karyoploteR, regioneR) by this command below. ``` BiocManager::install('[PACKAGE_NAME]') ``` + Requirements + R package list (version) + biomaRt (>=2.38.0) + GenomicRanges (>= 1.34.0) + ggplot2 (>=3.1.0) + grDevices (>=3.5.3) + karyoploteR (>=1.6.3) + openxlsx (>=4.1.4) + plyr (>=1.8.4) + RColorBrewer (>=1.1-2) + regioneR (>=1.12.0) + rtracklayer (>=1.42.2) + stats (>=3.5.3) + stringr (>=1.3.1) + utils (>=3.5.3) + Input format + BLAST (Same with outfmt = 6 of command-line BLAST) Column_name | Contents --------------- | --------------- qseqid | query sequence id sseqid | subject sequence id pident | percentage of identical matches length | alignment length mismatch | number of mismatches gapopen | number of gap openings qstart | start of alignment in query qend | end of alignment in query sstart | start of alignment in subject send | end of alignment in subject evalue | expect value bitscore | bit score + BLAT \*.psl format file + 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 [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] stringr_1.4.0 rtracklayer_1.42.2 RColorBrewer_1.1-2 plyr_1.8.5 [5] openxlsx_4.1.4 karyoploteR_1.8.8 regioneR_1.14.0 ggplot2_3.3.0 [9] GenomicRanges_1.34.0 GenomeInfoDb_1.18.2 IRanges_2.16.0 S4Vectors_0.20.1 [13] BiocGenerics_0.28.0 biomaRt_2.38.0 RIPAT_0.99.8 loaded via a namespace (and not attached): [1] ProtGenerics_1.14.0 bitops_1.0-6 matrixStats_0.55.0 [4] bit64_0.9-7 progress_1.2.2 httr_1.4.1 [7] tools_3.5.3 backports_1.1.5 R6_2.4.1 [10] rpart_4.1-13 lazyeval_0.2.2 Hmisc_4.3-1 [13] DBI_1.1.0 colorspace_1.4-1 nnet_7.3-12 [16] withr_2.1.2 tidyselect_1.0.0 gridExtra_2.3 [19] prettyunits_1.1.1 curl_4.3 bit_1.1-15.2 [22] compiler_3.5.3 Biobase_2.42.0 htmlTable_1.13.3 [25] bezier_1.1.2 DelayedArray_0.8.0 scales_1.1.0 [28] checkmate_2.0.0 digest_0.6.25 Rsamtools_1.34.1 [31] foreign_0.8-71 XVector_0.22.0 base64enc_0.1-3 [34] dichromat_2.0-0 pkgconfig_2.0.3 htmltools_0.4.0 [37] ensembldb_2.6.8 BSgenome_1.50.0 htmlwidgets_1.5.1 [40] rlang_0.4.5 rstudioapi_0.11 RSQLite_2.2.0 [43] BiocParallel_1.16.6 zip_2.0.4 acepack_1.4.1 [46] dplyr_0.8.4 VariantAnnotation_1.28.13 RCurl_1.98-1.1 [49] magrittr_1.5 GenomeInfoDbData_1.2.0 Formula_1.2-3 [52] Matrix_1.2-15 Rcpp_1.0.3 munsell_0.5.0 [55] bamsignals_1.14.0 lifecycle_0.2.0 stringi_1.4.6 [58] yaml_2.2.1 SummarizedExperiment_1.12.0 zlibbioc_1.28.0 [61] grid_3.5.3 blob_1.2.1 crayon_1.3.4 [64] lattice_0.20-38 Biostrings_2.50.2 splines_3.5.3 [67] GenomicFeatures_1.34.8 hms_0.5.3 knitr_1.28 [70] pillar_1.4.3 XML_3.99-0.3 glue_1.3.1 [73] biovizBase_1.30.1 latticeExtra_0.6-28 data.table_1.12.8 [76] vctrs_0.2.4 gtable_0.3.0 purrr_0.3.3 [79] assertthat_0.2.1 xfun_0.12 AnnotationFilter_1.6.0 [82] survival_3.1-8 tibble_3.0.1 GenomicAlignments_1.18.1 [85] AnnotationDbi_1.44.0 memoise_1.1.0 cluster_2.0.7-1 [88] ellipsis_0.3.0 ```