{"id":18466175,"url":"https://github.com/rainoffallingstar/erebor","last_synced_at":"2025-07-31T11:13:27.856Z","repository":{"id":233132591,"uuid":"779269991","full_name":"rainoffallingstar/ereboR","owner":"rainoffallingstar","description":null,"archived":false,"fork":false,"pushed_at":"2024-12-16T01:51:33.000Z","size":6196,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-05-05T14:54:10.201Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"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/rainoffallingstar.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,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2024-03-29T12:42:41.000Z","updated_at":"2024-12-16T01:51:36.000Z","dependencies_parsed_at":"2024-12-13T13:23:53.082Z","dependency_job_id":"e10855dc-7eb3-48b5-b9f0-7df406d3c013","html_url":"https://github.com/rainoffallingstar/ereboR","commit_stats":null,"previous_names":["rainoffallingstar/erebor"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/rainoffallingstar/ereboR","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rainoffallingstar%2FereboR","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rainoffallingstar%2FereboR/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rainoffallingstar%2FereboR/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rainoffallingstar%2FereboR/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/rainoffallingstar","download_url":"https://codeload.github.com/rainoffallingstar/ereboR/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rainoffallingstar%2FereboR/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":268028063,"owners_count":24183760,"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","status":"online","status_checked_at":"2025-07-31T02:00:08.723Z","response_time":66,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"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":[],"created_at":"2024-11-06T09:15:32.188Z","updated_at":"2025-07-31T11:13:27.835Z","avatar_url":"https://github.com/rainoffallingstar.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"---\noutput: github_document\n---\n\n\u003c!-- README.md is generated from README.Rmd. Please edit that file --\u003e\n\n```{r, include = FALSE}\nknitr::opts_chunk$set(\n  collapse = TRUE,\n  comment = \"#\u003e\"\n)\n```\n\n# erebor\n\n\u003cimg src=\"https://github.com/rainoffallingstar/ereboR/tree/master/dev/erebor.png\" height=\"200\" align=\"right\"/\u003e \u003c!-- badges: start --\u003e\n\n\u003c!-- badges: end --\u003e\n\nThe goal of erebor is to build a R6-based package for bulk RNAseq and RRBS analysis.\n\n## Installation\n\nYou can install the development version of sell:\n\n```{r install,eval=FALSE}\n# FILL THIS IN! HOW CAN PEOPLE INSTALL YOUR DEV PACKAGE?\npak::pak(\"rainoffallingstar/ereboR\")\n```\n\n## Example\n\nThis is a basic example which shows you how to solve a common problem:\n\n```{r example,eval=FALSE}\nlibrary(erebor)\n## the upstream analysis of RNA-seq\n\nBagginsClass$new(...)\n\n## the upstream analysis of RRBS\n\nSamwiseClass$new(...)\n\n### root_dir 是放bam文件的目录\n### 注意，这个包在运行结束后会将bam文件拷贝到processed目录\nsamwise \u003c- erebor::SamwiseClass$new(root_dir = \".\",\n                         methyratio_py = \"methratio.py\",\n                         gene_fa = \"Genedata/hg19.fa\")\n# 提取甲基化位点，并转化为bismark_cov格式,\n#可以指定一个装有python2.7的conda环境(如果不为NULL)\nsamwise$bam2methyratio(save2bismark = T,use_conda_env = \"py27\",\n                       cores = 16,\n                       mem = 100000)\n\n## download public data from TGCA/GEO\n\nlaml \u003c- MoriaClass$new(mine = \"TCGA-LAML\",Dwarf_worker = \"TGCA\")\n#laml$download()\n\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frainoffallingstar%2Ferebor","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Frainoffallingstar%2Ferebor","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frainoffallingstar%2Ferebor/lists"}