{"id":13637842,"url":"https://github.com/ShixiangWang/DoAbsolute","last_synced_at":"2025-04-19T17:32:01.699Z","repository":{"id":41807955,"uuid":"164417349","full_name":"ShixiangWang/DoAbsolute","owner":"ShixiangWang","description":":package: Automate Absolute Copy Number Calling using 'ABSOLUTE' package","archived":false,"fork":false,"pushed_at":"2023-11-28T03:13:40.000Z","size":2623,"stargazers_count":35,"open_issues_count":2,"forks_count":11,"subscribers_count":1,"default_branch":"master","last_synced_at":"2024-08-03T01:11:55.333Z","etag":null,"topics":["absolute","copy-number-variation","firehose"],"latest_commit_sha":null,"homepage":"","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/ShixiangWang.png","metadata":{"files":{"readme":"README.Rmd","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2019-01-07T10:39:28.000Z","updated_at":"2024-04-26T12:47:26.000Z","dependencies_parsed_at":"2023-11-28T04:30:31.257Z","dependency_job_id":"4b169144-3d06-44be-b2f8-cc877bb7ac12","html_url":"https://github.com/ShixiangWang/DoAbsolute","commit_stats":null,"previous_names":[],"tags_count":5,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ShixiangWang%2FDoAbsolute","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ShixiangWang%2FDoAbsolute/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ShixiangWang%2FDoAbsolute/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ShixiangWang%2FDoAbsolute/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ShixiangWang","download_url":"https://codeload.github.com/ShixiangWang/DoAbsolute/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":223804969,"owners_count":17205832,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["absolute","copy-number-variation","firehose"],"created_at":"2024-08-02T01:00:35.186Z","updated_at":"2024-11-09T08:30:24.017Z","avatar_url":"https://github.com/ShixiangWang.png","language":"R","readme":"---\noutput: github_document\n---\n\n\u003c!-- README.md is generated from README.Rmd. Please edit that file --\u003e\n\n```{r setup, include = FALSE}\nknitr::opts_chunk$set(\n  collapse = TRUE,\n  comment = \"#\u003e\",\n  fig.path = \"man/figures/README-\",\n  out.width = \"100%\"\n)\n```\n\n# DoAbsolute\n\n[![lifecycle](https://img.shields.io/badge/lifecycle-stable-blue.svg)](https://www.tidyverse.org/lifecycle/#stable)\n[![GitHub\ntag](https://img.shields.io/github/tag/ShixiangWang/DoAbsolute.svg?label=Github)](https://github.com/ShixiangWang/DoAbsolute)\n[![Hits](https://hits.seeyoufarm.com/api/count/incr/badge.svg?url=https%3A%2F%2Fgithub.com%2FShixiangWang%2FDoAbsolute\u0026count_bg=%2379C83D\u0026title_bg=%23555555\u0026icon=\u0026icon_color=%23E7E7E7\u0026title=hits\u0026edge_flat=false)](https://hits.seeyoufarm.com)\n\nThe goal of **DoAbsolute** is to automate ABSOLUTE calling for multiple\nsamples in batch-processing.\n\n\u003e  **Running this tool with 1 thread (default setting) is highly recommended**, see [note!!!](#note)!\n\n[ABSOLUTE](https://www.nature.com/articles/nbt.2203) is a famous\nsoftware developed by Broad Institute, however, the `RunAbsolute`\nfunction is designed for computing one sample each time and set no\ndefault values. **DoAbsolute** helps user set default parameters\naccording to [ABSOLUTE\ndocumentation](http://software.broadinstitute.org/cancer/software/genepattern/modules/docs/ABSOLUTE),\nprovides a uniform interface to input data easily and runs **RunAbsolute**\nparallelly.\n\nMore detail about how to analyze ABSOLUTE results please see [this link](http://software.broadinstitute.org/cancer/software/genepattern/analyzing-absolute-data).\n\n## Installation\n\nYou can install the released version of DoAbsolute with:\n\n``` r\n# Option 1: GitHub\ndevtools::install_github(\"ShixiangWang/DoAbsolute\")\n\n\n# Option 2: r-universe\n#\n# Enable repository from shixiangwang\noptions(repos = c(\n  shixiangwang = 'https://shixiangwang.r-universe.dev',\n  CRAN = 'https://cloud.r-project.org'))\ninstall.packages('DoAbsolute')\n```\n\nInstall ABSOLUTE, the version provided by DoAbsolute is 1.0.6. You can\nfind available versions at \u003chttps://software.broadinstitute.org/cancer/cga/absolute_download\u003e.\nUsers of DoAbsolute all should accept LICENCE from Firehorse.\n\n```r\ninstall.packages(\"numDeriv\")\npath_to_file = system.file(\"extdata\", \"ABSOLUTE_1.0.6.tar.gz\", package = \"DoAbsolute\", mustWork = T)\ninstall.packages(path_to_file, repos = NULL, type=\"source\")\n```\n\n\u003e NOTE: the builtin ABSOLUTE package is modified for fitting current R version\n\u003e and reducing some errors (this may be described in NEWS.md).\n\u003e If you want to use the raw package without modification, you can find it\n\u003e [here](https://github.com/ShixiangWang/DoAbsolute/wiki/ABSOLUTE-raw-package).\n\u003e Remember the raw package (v1.0.6) is only working under R4.2.\n\n## Example\n\nThis is a basic example which shows you how to run DoAbsolute using example data\nfrom [ABSOLUTE documentation](http://software.broadinstitute.org/cancer/software/genepattern/modules/docs/ABSOLUTE).\n\nLoad package.\n\n\n```{r, eval=FALSE}\nlibrary(DoAbsolute)\n```\n\n\n```{r example, eval=F}\nexample_path = system.file(\"extdata\", package = \"DoAbsolute\", mustWork = T)\n\n\nlibrary(data.table)\n# Load Test Data ----------------------------------------------------------\n\n# segmentation file\nseg_normal =  file.path(example_path, \"SNP6_blood_normal.seg.txt\")\nseg_solid  =  file.path(example_path, \"SNP6_solid_tumor.seg.txt\")\nseg_metastatic  = file.path(example_path, \"SNP6_metastatic_tumor.seg.txt\")\n# MAF file\nmaf_solid  = file.path(example_path, \"solid_tumor.maf.txt\")\nmaf_metastatic  = file.path(example_path, \"metastatic_tumor.maf.txt\")\n\n# read data\nseg_normal = fread(seg_normal)\nseg_solid = fread(seg_solid)\nseg_metastatic = fread(seg_metastatic)\nmaf_solid = fread(maf_solid)\nmaf_metastatic = fread(maf_metastatic)\n\n# merge data\nSeg = Reduce(rbind, list(seg_normal, seg_solid, seg_metastatic))\nMaf = Reduce(rbind, list(maf_solid, maf_metastatic))\n\nSeg$Sample = substr(Seg$Sample, 1, 15)\nMaf$Tumor_Sample_Barcode = substr(Maf$Tumor_Sample_Barcode, 1, 15)\n\n# test function\nDoAbsolute(Seg = Seg, Maf = Maf, platform = \"SNP_6.0\", copy.num.type = \"total\",\n           results.dir = \"test\", keepAllResult = TRUE, verbose = TRUE)\n```\n\n## NOTE!!!\n\nSome inconsistent results have been reported in some issues (See discussion in \u003chttps://github.com/ShixiangWang/DoAbsolute/issues/23\u003e and \u003chttps://github.com/ShixiangWang/DoAbsolute/issues/26\u003e), and it possibly relates to the parallel computation backend. **So, at default, run this tool with only 1 thread is highly recommended**!\n\n\n## Citation\n\n```\nWang, Shixiang, et al. \"The predictive power of tumor mutational burden \n    in lung cancer immunotherapy response is influenced by patients' sex.\" \n    International journal of cancer (2019).\n```\n\nReference:\n\n* Carter, Scott L., et al. \"Absolute quantification of somatic DNA alterations in human cancer.\" Nature biotechnology 30.5 (2012): 413.\n","funding_links":[],"categories":["Genomics"],"sub_categories":["Mutations"],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FShixiangWang%2FDoAbsolute","html_url":"https://awesome.ecosyste.ms/projects/github.com%2FShixiangWang%2FDoAbsolute","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FShixiangWang%2FDoAbsolute/lists"}