[{"_1":2,"_184":-5,"_185":-5},"loaderData",{"_3":4,"_13":14,"_21":22,"_159":160},"root",{"_5":-5,"_6":-7,"_7":8,"_9":-7,"_10":11,"_12":-7},"currentUser","primaryEmail","siteVerification","6LeIxAcTAAAAAJcZVRqyHh71UMIEGNQ_MXjiZKhI","toast","enableDev",false,"incidentStatus","routes/_layout",{"_15":-5,"_16":17,"_18":17,"_19":11,"_20":11},"username","isAskGordonEnabled",true,"isUsingNewTemplate","showMinimalLanding","showHoneypotTrap","routes/_layout.r.$namespace.$reponame",{"_23":24,"_25":-5,"_26":11,"_27":11,"_28":29,"_30":31,"_32":-5,"_33":11,"_34":35,"_84":85,"_104":105,"_152":-5,"_153":11,"_154":17,"_155":11,"_156":-5,"_157":158},"canonicalUrl","https://hub.docker.com/r/scrnaseqbenchmark/scmap/tags","mcpServer","canSeeDockerfile","canSeeAutobuilds","namespace","scrnaseqbenchmark","reponame","scmap","cloudBuildSource","isAutobuildsAvailable","repo",{"_36":37,"_38":39,"_41":42,"_43":44,"_45":11,"_46":47,"_48":49,"_50":51,"_53":31,"_28":29,"_54":55,"_56":40,"_57":58,"_59":60,"_61":62,"_63":-5,"_64":58,"_65":66,"_67":11,"_68":29,"_69":70,"_75":11,"_76":77,"_81":29,"_82":83},"categories",[],"content_types",[40],"image","date_registered","2019-06-27T12:02:34.440011Z","description","","is_private","last_updated","2019-08-02T14:57:12.82877Z","last_modified","2024-10-16T13:48:34.145251Z","media_types",[52],"application/vnd.docker.container.image.v1+json","name","pull_count",516,"repository_type","star_count",0,"status",1,"status_description","active","source","collaborator_count","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",{"_71":11,"_72":73},"enabled","rules",[74],".*","is_automated","permissions",{"_78":17,"_79":11,"_80":11},"read","write","admin","user","storage_size",1038782455,"orgData",{"_86":87,"_88":89,"_90":91,"_92":29,"_93":44,"_94":44,"_95":96,"_97":44,"_98":99,"_100":44,"_101":44,"_102":44,"_103":17},"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",[106,142],{"_107":40,"_108":109,"_110":111,"_86":112,"_113":114,"_46":131,"_132":109,"_133":29,"_134":52,"_53":135,"_136":137,"_138":122,"_139":131,"_140":62,"_141":17},"content_type","creator",6267062,"full_size",442895192,60277702,"images",[115],{"_116":117,"_118":119,"_120":44,"_121":122,"_123":124,"_125":126,"_127":44,"_128":-5,"_129":111,"_59":62,"_130":-5},"architecture","amd64","digest","sha256:d20ca59f96eb0016c7d4dcba1641ab8b4bff179bb26bffce71c6f40731c85277","features","last_pulled","2026-09-13T21:33:24.21486164Z","last_pushed","2019-08-02T13:04:42Z","os","linux","os_features","os_version","size","variant","2019-08-02T14:57:12.549971Z","last_updater","last_updater_username","media_type","latest","repository",7326841,"tag_last_pulled","tag_last_pushed","tag_status","v2",{"_107":40,"_108":109,"_110":143,"_86":144,"_113":145,"_46":150,"_132":109,"_133":29,"_134":52,"_53":151,"_136":137,"_138":148,"_139":150,"_140":62,"_141":17},431274659,60749257,[146],{"_116":117,"_118":147,"_120":44,"_121":148,"_123":149,"_125":126,"_127":44,"_128":-5,"_129":143,"_59":62,"_130":-5},"sha256:d113cf2347c884470c8c1ed707af73c734dfac9826052498479ac4d8dd6a5c9c","2026-09-13T21:33:25.080044625Z","2019-07-02T16:17:10Z","2019-07-02T16:17:09.935795Z","pipeline_0.1","sbxKitMetadata","isPotentialSpam","isHubSbxKitsEnabled","displaySecurityMetadata","tagAttestations","tagsHaveAttestations",[],"routes/_layout.r.$namespace.$reponame.tags",{"_34":161,"_168":169,"_157":182,"_183":11},{"_36":162,"_38":163,"_41":42,"_43":44,"_45":11,"_46":47,"_48":49,"_50":164,"_53":31,"_28":29,"_54":55,"_56":40,"_57":58,"_59":60,"_61":62,"_63":-5,"_64":58,"_65":66,"_67":11,"_68":29,"_69":165,"_75":11,"_76":167,"_81":29,"_82":83},[],[40],[52],{"_71":11,"_72":166},[74],{"_78":17,"_79":11,"_80":11},"tags",{"_170":171,"_172":-5,"_173":-5,"_174":175},"count",2,"next","previous","results",[176,179],{"_107":40,"_108":109,"_110":111,"_86":112,"_113":177,"_46":131,"_132":109,"_133":29,"_134":52,"_53":135,"_136":137,"_138":122,"_139":131,"_140":62,"_141":17},[178],{"_116":117,"_118":119,"_120":44,"_121":122,"_123":124,"_125":126,"_127":44,"_128":-5,"_129":111,"_59":62,"_130":-5},{"_107":40,"_108":109,"_110":143,"_86":144,"_113":180,"_46":150,"_132":109,"_133":29,"_134":52,"_53":151,"_136":137,"_138":148,"_139":150,"_140":62,"_141":17},[181],{"_116":117,"_118":147,"_120":44,"_121":148,"_123":149,"_125":126,"_127":44,"_128":-5,"_129":143,"_59":62,"_130":-5},[],"canDeleteTags","actionData","errors"]

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