[{"_1":2,"_192":-5,"_193":-5},"loaderData",{"_3":4,"_17":18,"_25":26,"_168":169},"root",{"_5":-5,"_6":-7,"_7":8,"_9":-7,"_10":11,"_12":-7,"_13":14,"_15":16},"currentUser","primaryEmail","siteVerification","6LeIxAcTAAAAAJcZVRqyHh71UMIEGNQ_MXjiZKhI","toast","enableDev",false,"incidentStatus","theme","system","contrast","normal","routes/_layout",{"_19":-5,"_20":21,"_22":21,"_23":11,"_24":21},"username","isAskGordonEnabled",true,"isUsingNewTemplate","showMinimalLanding","showHoneypotTrap","routes/_layout.r.$namespace.$reponame",{"_27":28,"_29":-5,"_30":11,"_31":11,"_32":33,"_34":35,"_36":-5,"_37":11,"_38":39,"_89":90,"_109":110,"_157":-5,"_158":11,"_159":21,"_160":11,"_161":-5,"_162":11,"_163":-5,"_164":165,"_166":111,"_167":-7},"canonicalUrl","https://hub.docker.com/r/scrnaseqbenchmark/cell_blast/tags","mcpServer","canSeeDockerfile","canSeeAutobuilds","namespace","scrnaseqbenchmark","reponame","cell_blast","cloudBuildSource","isAutobuildsAvailable","repo",{"_40":41,"_42":43,"_45":46,"_47":48,"_49":11,"_50":51,"_52":53,"_54":55,"_57":35,"_32":33,"_58":59,"_60":44,"_61":62,"_63":64,"_65":66,"_67":-5,"_68":69,"_70":71,"_72":11,"_73":33,"_74":75,"_80":11,"_81":82,"_86":33,"_87":88},"categories",[],"content_types",[44],"image","date_registered","2019-06-27T09:03:11.961578Z","description","","is_private","last_updated","2019-08-02T15:20:45.866389Z","last_modified","2024-10-16T13:48:34.145251Z","media_types",[56],"application/vnd.docker.container.image.v1+json","name","pull_count",435,"repository_type","star_count",2,"status",1,"status_description","active","source","collaborator_count",0,"full_description","# scRNAseq_Benchmark\nBenchmarking classification tools for scRNA-seq data\n\n## How to use\n[snakemake](https://snakemake.readthedocs.io/en/stable/index.html) and\n[singularity](https://www.sylabs.io/docs/) need to be available on your system.\n\nFrom the root of this repository:\n```\nsnakemake \\\n --configfile \\\n --use-singularity\n```\n\nIf your data or output directory is not located under the root of this\nrepository, be sure to tell snakemake to mount the appropriate directories\nin singularity:\n```\nsnakemake \\\n --configfile \\\n --use-singularity \\\n --singularity-args '--bind : --bind :'\n```\n\n#### The config file\n```YML\noutput_dir: \ndatafile: \nlabfile: \ncolumn: \nnumber_of_features: \ngenes: \nhuman: \ntools_to_run: # List of tools to run\n - \n - \n - <...>\n```\n\n##### Tool specific inputs\nSome tools require specific inputs. Add the following to your config file when\none of these tools:\n- Garnett_CV\n ```YML\n Garnett_CV:\n markers: \n ```\n- Garnett_Pretrained\n ```YML\n Garnett_Pretrained:\n classifier: \n ```\n\n\n\n## Included tools/methods\n- kNN50\n- kNN9\n- LDA\n- LDA_rejection (LDA with rejection option)\n- NMC\n- RF\n- SVM\n- SVM (SVM with rejection option)\n- [singleCellNet](https://github.com/pcahan1/singleCellNet)\n- [CHETAH](https://github.com/jdekanter/CHETAH)\n- [scmap](https://github.com/hemberg-lab/scmap)\n - scmapcell\n - scmapcluster\n- [SingleR](https://github.com/dviraran/SingleR)\n- [scID](https://github.com/BatadaLab/scID)\n- [scVI](https://github.com/YosefLab/scVI)\n- [Cell_BLAST](https://github.com/gao-lab/Cell_BLAST)\n- [Garnett](https://cole-trapnell-lab.github.io/garnett/)\n - Garnett_CV (without pretrained classifier)\n - Garnett_Pretrained (with pretrained classifier)\n\n## Adding new tools\nIn order to add a tool to this benchmarking workflow, a rule for this tool\nneeds to be added to the `Snakefile`. This rule should produce as output:\n- a table of predicted label (`/_pred.csv`).\n- a table of true labels (`/_true.csv`).\n- a tables of testing, prediction and/or total time:\n - `//_test_time.csv`\n - `//_training_time.csv`\n - `//_total_time.csv`\n\nThe input to this rule should be:\n- a count table (specified as the `datafile` in the config).\n- a true labels file (specified as the `labfile` in the config).\n\nYou will want to write a wrapper script for the tool you want to\nadd to facilitate this. The `\"{output_dir}/CV_folds.RData\"` input may be\nused to provide your wrapper script with folds for cross_validation.\nIt is recommended to make a docker image containing all dependencies for both\nthe tool and any wrappers for the tool. \nThis wrapper script should also make a selection of the features to be used.\nThis selection should be based on ranking which can be accessed by providing\n`feature ranking` as input to the wrapper script. The number of features to be\nused should be configurable and settable through the 'number_of_features' field\nin the config.\n\nThe following can be used as a template for new rules. Replace everything\nsurrounded by (and including the) `<>` with appropriate values.\n```\nrule SVM:\n input:\n datafile = config[\"datafile\"],\n labfile = config[\"labfile\"],\n folds = \"{output_dir}/CV_folds.RData\",\n ranking = feature_ranking\n output:\n pred = \"{output_dir}//_pred.csv\",\n true = \"{output_dir}//_true.csv\",\n test_time = \"{output_dir}//_test_time.csv\",\n training_time = \"{output_dir}//_training_time.csv\"\n log: \"{output_dir}//.log\"\n params:\n n_features = config.get(\"number_of_features\", 0)\n singularity: \"docker://\"\n shell:\n \" \"\n \"{input.datafile} \"\n \"{input.labfile} \"\n \"{input.folds} \"\n \"{wildcards.output_dir}/ \"\n \"{input.ranking} \"\n \"{params.n_features} \"\n \"&> {log}\"\n```\n","has_starred","hub_user","immutable_tags_settings",{"_76":11,"_77":78},"enabled","rules",[79],".*","is_automated","permissions",{"_83":21,"_84":11,"_85":11},"read","write","admin","user","storage_size",2048034852,"orgData",{"_91":92,"_93":94,"_95":96,"_97":33,"_98":48,"_99":48,"_100":101,"_102":48,"_103":104,"_105":48,"_106":48,"_107":48,"_108":21},"id","53d6bc35d06343c1b0caa2967dd5c7ea","uuid","53d6bc35-d063-43c1-b0ca-a2967dd5c7ea","type","organization","orgname","full_name","location","company","LUMC","profile_url","date_joined","2019-05-07T08:33:55.628431Z","gravatar_url","gravatar_email","badge","is_active","recentTags",[111,147],{"_112":44,"_113":114,"_115":116,"_91":117,"_118":119,"_50":136,"_137":114,"_138":33,"_139":56,"_57":140,"_141":142,"_143":127,"_144":136,"_145":66,"_146":21},"content_type","creator",6267062,"full_size",540249437,60259511,"images",[120],{"_121":122,"_123":124,"_125":48,"_126":127,"_128":129,"_130":131,"_132":48,"_133":-5,"_134":116,"_63":66,"_135":-5},"architecture","amd64","digest","sha256:c5e13ab310c27c41605c7e006dd35780d27816a3a725c63e54856a2699352638","features","last_pulled","2026-09-30T09:13:39.757640632Z","last_pushed","2019-08-01T15:49:02Z","os","linux","os_features","os_version","size","variant","2019-08-02T15:20:45.536221Z","last_updater","last_updater_username","media_type","latest","repository",7325819,"tag_last_pulled","tag_last_pushed","tag_status","v2",{"_112":44,"_113":114,"_115":148,"_91":149,"_118":150,"_50":155,"_137":114,"_138":33,"_139":56,"_57":156,"_141":142,"_143":153,"_144":155,"_145":66,"_146":21},574304111,60742280,[151],{"_121":122,"_123":152,"_125":48,"_126":153,"_128":154,"_130":131,"_132":48,"_133":-5,"_134":148,"_63":66,"_135":-5},"sha256:9185d7a05a903c279ab396e25c09c49ced3c2e9701f14b140c925be67772c0e3","2026-09-17T15:23:08.023793271Z","2019-07-02T15:18:17Z","2019-07-02T15:18:16.534698Z","pipeline_0.1","sbxKitMetadata","isPotentialSpam","isHubSbxKitsEnabled","showSbxLogoOverride","sbxTrademarkText","displaySecurityMetadata","tagAttestations","tagsHaveAttestations",[],"selectedTag","attestationsUrl","routes/_layout.r.$namespace.$reponame.tags",{"_38":170,"_177":178,"_164":190,"_191":11},{"_40":171,"_42":172,"_45":46,"_47":48,"_49":11,"_50":51,"_52":53,"_54":173,"_57":35,"_32":33,"_58":59,"_60":44,"_61":62,"_63":64,"_65":66,"_67":-5,"_68":69,"_70":71,"_72":11,"_73":33,"_74":174,"_80":11,"_81":176,"_86":33,"_87":88},[],[44],[56],{"_76":11,"_77":175},[79],{"_83":21,"_84":11,"_85":11},"tags",{"_179":62,"_180":-5,"_181":-5,"_182":183},"count","next","previous","results",[184,187],{"_112":44,"_113":114,"_115":116,"_91":117,"_118":185,"_50":136,"_137":114,"_138":33,"_139":56,"_57":140,"_141":142,"_143":127,"_144":136,"_145":66,"_146":21},[186],{"_121":122,"_123":124,"_125":48,"_126":127,"_128":129,"_130":131,"_132":48,"_133":-5,"_134":116,"_63":66,"_135":-5},{"_112":44,"_113":114,"_115":148,"_91":149,"_118":188,"_50":155,"_137":114,"_138":33,"_139":56,"_57":156,"_141":142,"_143":153,"_144":155,"_145":66,"_146":21},[189],{"_121":122,"_123":152,"_125":48,"_126":153,"_128":154,"_130":131,"_132":48,"_133":-5,"_134":148,"_63":66,"_135":-5},[],"canDeleteTags","actionData","errors"]

scrnaseqbenchmark/cell_blast

Tags for scrnaseqbenchmark/cell_blast