{"id":17671411,"url":"https://github.com/nbenn/singlecellfeatures","last_synced_at":"2025-03-30T15:20:43.614Z","repository":{"id":29259950,"uuid":"32792562","full_name":"nbenn/singleCellFeatures","owner":"nbenn","description":null,"archived":false,"fork":false,"pushed_at":"2016-06-15T09:13:30.000Z","size":85010,"stargazers_count":1,"open_issues_count":1,"forks_count":0,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-02-05T16:48:22.333Z","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":"nats-io/java-nats-streaming","license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/nbenn.png","metadata":{"files":{"readme":"readme.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2015-03-24T10:47:02.000Z","updated_at":"2017-07-30T23:14:43.000Z","dependencies_parsed_at":"2022-09-06T14:52:10.417Z","dependency_job_id":null,"html_url":"https://github.com/nbenn/singleCellFeatures","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nbenn%2FsingleCellFeatures","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nbenn%2FsingleCellFeatures/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nbenn%2FsingleCellFeatures/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nbenn%2FsingleCellFeatures/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/nbenn","download_url":"https://codeload.github.com/nbenn/singleCellFeatures/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":246334891,"owners_count":20760736,"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":[],"created_at":"2024-10-24T03:42:25.259Z","updated_at":"2025-03-30T15:20:43.586Z","avatar_url":"https://github.com/nbenn.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# singleCellFeatures\nThis R package serves to acquire and analyse single cell feature data as generated and compiled by TargetInfectX. The data is produced by [iBRAIN2](http://www.infectx.org/about_us/iBRAIN2/) based image analysis workflow and is hosted in an [openBIS](http://www.targetinfectx.ch/about_us/openBIS/) instance.\n\n## Installation\nThe easiest way is throught the `install_github` functionality of the devtools package:\n\n```R\ninstall.packages(\"devtools\")\nlibrary(devtools)\n\ninstall_github(\"nbenn/singleCellFeatures\")\n```\n\nAlternatively the package can be [downloaded](https://github.com/nbenn/singleCellFeatures/archive/master.zip) and installed manually:\n\n```bash\nunzip ~/Downloads/singleCellFeatures-master.zip\nR CMD INSTALL --no-multiarch --with-keep.source ~/Downloads/singleCellFeatures-master\n```\n\n## Configuration\nSome setup dependent information has to be provided, all of which is stored in a yaml file. The default location of this config file is `~/.singleCellFeaturesConfig`. This can be changed on a per-session basis using the function `configPathSet()` of more permanently, using an `.Rprofile` file.\n\n```R\n## if no config file is present, set one up\n# set the config file location\nconfigPathSet(\"path/to/where/you/want/your/config.yaml\")\n# create a template file\nconfigInit()\n# using a text editor, modify this file for your system\n\n## for inter-session persistence, add the following to your .Rprofile\noptions(singleCellFeatures.configPath = \"path/to/your/config.yaml\")\n```\n\nThe config file has the following structure:\n\n```yaml\ndataStorage:\n  dataDir: \"/path/to/data/dir\"\n  metaDir: \"/path/to/metadata/dir\"\nbeeDownloader:\n  executable: \"/path/to/repo/openBIS/Tools/BeeDataSetDownloader\"\nopenBIS:\n  username: \"user\"\n  password: \"password\"\nsingleCellFeatures:\n  sourceDir: \"/path/to/source\"\n```\n\nThe two entries under `dataStorage` should be located on a volume with a couple of GB of free storage, to be able to hold a couple of plates. A complete plate uses 1-2 GB of storage, so having upwards of 50 GB available is recommended. The two entries under `beeDownloader` are concerned with `BeeDataSetDownloader`. More information available [here](https://wiki.systemsx.ch/pages/viewpage.action?title=InfectX+Single+Cell+Data+Access\u0026spaceKey=InfectXRTD). The final section holds the path to the local source of this package. It is only used to update the databases in `/data` (see the `utilDatabase.R` file).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnbenn%2Fsinglecellfeatures","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fnbenn%2Fsinglecellfeatures","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnbenn%2Fsinglecellfeatures/lists"}