{"id":22021694,"url":"https://github.com/lieberinstitute/brainstorm","last_synced_at":"2026-02-13T06:42:13.612Z","repository":{"id":113731861,"uuid":"337530751","full_name":"LieberInstitute/brainstorm","owner":"LieberInstitute","description":"Matching genotype and RNA-seq data to conform IDs of brain samples","archived":false,"fork":false,"pushed_at":"2024-12-10T20:56:45.000Z","size":3438,"stargazers_count":2,"open_issues_count":5,"forks_count":1,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-10-11T06:32:09.693Z","etag":null,"topics":["genotype","quality-control","rna-seq","rstats"],"latest_commit_sha":null,"homepage":"http://research.libd.org/brainstorm/","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/LieberInstitute.png","metadata":{"files":{"readme":"README.Rmd","changelog":"NEWS.md","contributing":null,"funding":null,"license":null,"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":"2021-02-09T20:41:02.000Z","updated_at":"2024-12-10T20:56:50.000Z","dependencies_parsed_at":"2025-01-28T16:44:41.848Z","dependency_job_id":"e5231158-0e2b-46e5-8cce-3316cdbfbb07","html_url":"https://github.com/LieberInstitute/brainstorm","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/LieberInstitute/brainstorm","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LieberInstitute%2Fbrainstorm","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LieberInstitute%2Fbrainstorm/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LieberInstitute%2Fbrainstorm/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LieberInstitute%2Fbrainstorm/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/LieberInstitute","download_url":"https://codeload.github.com/LieberInstitute/brainstorm/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LieberInstitute%2Fbrainstorm/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29398144,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-13T06:24:03.484Z","status":"ssl_error","status_checked_at":"2026-02-13T06:23:12.830Z","response_time":78,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":["genotype","quality-control","rna-seq","rstats"],"created_at":"2024-11-30T06:13:43.258Z","updated_at":"2026-02-13T06:42:13.585Z","avatar_url":"https://github.com/LieberInstitute.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    fig.path = \"man/figures/README-\",\n    out.width = \"100%\"\n)\n```\n\n# brainstorm\n\n\u003c!-- badges: start --\u003e\n[![Codecov test coverage](https://codecov.io/gh/LieberInstitute/brainstorm/branch/master/graph/badge.svg)](https://codecov.io/gh/LieberInstitute/brainstorm?branch=master)\n[![R-CMD-check-bioc](https://github.com/LieberInstitute/brainstorm/actions/workflows/check-bioc.yml/badge.svg)](https://github.com/LieberInstitute/brainstorm/actions/workflows/check-bioc.yml)\n\u003c!-- badges: end --\u003e\n\nThe goal of `brainstorm` is to match genotype and RNA-seq data to conform IDs of brain samples.\n\n## Installation instructions\n\nGet the latest stable `R` release from [CRAN](http://cran.r-project.org/). Then install `brainstorm` from [Bioconductor](http://bioconductor.org/) using the following code:\n\n```{r 'install', eval = FALSE}\nif (!requireNamespace(\"BiocManager\", quietly = TRUE)) {\n    install.packages(\"BiocManager\")\n}\n\nBiocManager::install(\"brainstorm\")\n```\n\nAnd the development version from [GitHub](https://github.com/) with:\n\n```{r 'install_dev', eval = FALSE}\nBiocManager::install(\"joshstolz/brainstorm\")\n```\n\n## Workflow \n\n### Step 1. Prepare the snp Data  \n\n![Data Prep](images/flow_data_prep.png)  \n\n### Step 2. Correlate the Data and Identify Groups \n\n![Correlation \u0026 Grouping](images/flow_cor_group.png)  \n\n\n\n### Step 3. Identify and Resolve Swaps\n\nComing Soon...\n\n## Example\n\n### TBD...\n\n```{r example, eval = requireNamespace('brainstorm')}\nlibrary(\"brainstorm\")\n## basic example code\n```\n\n## Citation\n\nBelow is the citation output from using `citation('brainstorm')` in R. Please\nrun this yourself to check for any updates on how to cite __brainstorm__.\n\n```{r 'citation', eval = requireNamespace('brainstorm')}\nprint(citation(\"brainstorm\"), bibtex = TRUE)\n```\n\nPlease note that the `brainstorm` was only made possible thanks to many other R and bioinformatics software authors, which are cited either in the vignettes and/or the paper(s) describing this package.\n\n## Code of Conduct\n\nPlease note that the `brainstorm` project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.\n\n## Development tools\n\n* Continuous code testing is possible thanks to [GitHub actions](https://www.tidyverse.org/blog/2020/04/usethis-1-6-0/)  through `r BiocStyle::CRANpkg('usethis')`, `r BiocStyle::CRANpkg('remotes')`, and `r BiocStyle::CRANpkg('rcmdcheck')` customized to use [Bioconductor's docker containers](https://www.bioconductor.org/help/docker/) and `r BiocStyle::Biocpkg('BiocCheck')`.\n* Code coverage assessment is possible thanks to [codecov](https://codecov.io/gh) and `r BiocStyle::CRANpkg('covr')`.\n* The [documentation website](http://.github.io/brainstorm) is automatically updated thanks to `r BiocStyle::CRANpkg('pkgdown')`.\n* The code is styled automatically thanks to `r BiocStyle::CRANpkg('styler')`.\n* The documentation is formatted thanks to `r BiocStyle::CRANpkg('devtools')` and `r BiocStyle::CRANpkg('roxygen2')`.\n\nFor more details, check the `dev` directory.\n\nThis package was developed using `r BiocStyle::Biocpkg('biocthis')`.\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flieberinstitute%2Fbrainstorm","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flieberinstitute%2Fbrainstorm","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flieberinstitute%2Fbrainstorm/lists"}