{"id":24528993,"url":"https://github.com/saezlab/bradiplus","last_synced_at":"2025-08-25T12:12:04.034Z","repository":{"id":23137892,"uuid":"26492979","full_name":"saezlab/BraDiPluS","owner":"saezlab","description":"BraDiPluS (Braille Display Plugs Data Analysis) is an R package to process and analyse data produced using the microfluidic platform for functional drug screening of patient biopsies developed in collaboration with Merten group (EMBL).","archived":false,"fork":false,"pushed_at":"2018-07-12T13:00:02.000Z","size":5267,"stargazers_count":2,"open_issues_count":2,"forks_count":3,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-08-10T06:38:32.786Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/saezlab.png","metadata":{"files":{"readme":"README.md","changelog":"ChangeLog.txt","contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2014-11-11T16:15:08.000Z","updated_at":"2024-05-04T01:18:07.000Z","dependencies_parsed_at":"2022-07-31T07:17:59.667Z","dependency_job_id":null,"html_url":"https://github.com/saezlab/BraDiPluS","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/saezlab/BraDiPluS","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2FBraDiPluS","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2FBraDiPluS/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2FBraDiPluS/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2FBraDiPluS/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/saezlab","download_url":"https://codeload.github.com/saezlab/BraDiPluS/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2FBraDiPluS/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":272063217,"owners_count":24866673,"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":"2025-08-25T02:00:12.092Z","response_time":1107,"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":"2025-01-22T07:34:19.670Z","updated_at":"2025-08-25T12:12:03.991Z","avatar_url":"https://github.com/saezlab.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"BraDiPluS\n=========\n\nBraDiPluS - Braille Display Plugs Data Analysis - is an R package developed to analyse the data of plugs produced using in-house combinatorial microfluidics platform and adquired using an in-house LabVIEW program (written by R. Utharala) allowing the detection of three channels:\n* _blue_: sample barcodes\n* _green_: Caspase-3 activity assay\n* _orange_: marker dye to monitor mixing of reagents \n\nFor extended documentation of BraDiPluS please refer to https://saezlab.github.io/BraDiPluS/ \n\n## How to install it\n\nOpen R and, from the folder with the package, type:\n\n```\ninstall.packages('BraDiPluS',repos=NULL,type='src')\n```\n\n## Workflow example\n\nLoad the example data provided in the package\n\n```\ndata(\"BxPC3_data\", package=\"BraDiPluS\")\ndata(\"sampleNames\", package=\"BraDiPluS\")\n```\n\nplot the data\n\n```\nplotData(data=MyData, channels=c(\"blue\", \"orange\", \"green\"))\n```\n\nseparate the different samples (separated by barcode) \n\n```\nres \u003c- samplesSelection(data=MyData, BCchannel=\"blue\",BCthr=0.01, BCminLength=100, distThr=16, plotMyData=F, barcodePos=\"before\")\nsamples\u003c-res$samples\nnames(samples)\u003c-sampleNames\n\nplotData(data=MyData, channels=c(\"blue\", \"orange\", \"green\"), samples = samples)\n```\n\nselect the peaks for each sample\n```\nsamplesPeaks \u003c- selectSamplesPeaks(samples, channel=\"green\", metric=\"median\", baseThr=0.01, minLength=350, discartPeaks=\"first\", discartPeaksPerc=5)\n```\n\nremove outliers based on orange channel\n```\nruns\u003c-list(run1=samplesPeaks)\nruns.qa\u003c-qualityAssessment(runs=runs)\n```\n\nlook at the median sample values\n```\nallData\u003c-do.call(cbind, lapply(runs.qa, function(myRun){\nsapply(sapply(myRun, get, x=\"green\"), median)\n}))\n```\n\ncompute z-score\n```\nallData_scale\u003c-apply(allData,2,scale)\n```\n\n\n![alt text](https://s-media-cache-ak0.pinimg.com/564x/50/0a/43/500a43906dea54dbff4d81d9ab7dfb23.jpg \"BraDiPluS\")\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsaezlab%2Fbradiplus","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsaezlab%2Fbradiplus","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsaezlab%2Fbradiplus/lists"}