{ "_id": "6a281afaa476d7de6d3c57c6", "Package": "IntegratedLearner", "Type": "Package", "Title": "Integrated Multi-Omics Learning for Survival and Other Outcomes", "Version": "0.99.0", "Authors@R": "c(\nperson(\"Nalin\", \"Arora\", email = \"naa4050@med.cornell.edu\",\nrole = c(\"aut\", \"cre\", \"cph\"),\ncomment = c(ORCID = \"0009-0009-1340-688X\")),\nperson(\"Anupreet\", \"Porwal\", role = \"aut\"),\nperson(\"Himel\", \"Mallick\", email = \"him4004@med.cornell.edu\", role = \"aut\")\n)", "Description": "Provides a unified interface for multi-omics prediction\nusing early, late, and intermediate fusion for continuous,\nbinary, multiclass, and survival outcomes. It supports both\nMultiAssayExperiment and PCL-style inputs, performs input\nvalidation and feature/sample harmonization across layers, and\nprovides model fitting, prediction, plotting, and\nvariable-importance utilities.", "License": "MIT + file LICENSE", "URL": "https://github.com/himelmallick/IntegratedLearner", "BugReports": "https://github.com/himelmallick/IntegratedLearner/issues", "Encoding": "UTF-8", "SystemRequirements": "Java (optional; required for SL.BART / bartMachine\nworkflows)", "VignetteBuilder": "knitr", "biocViews": "Software, Classification, Survival, Microbiome", "Config/testthat/edition": "3", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "8.0.0", "Config/pak/sysreqs": "default-jdk libicu-dev zlib1g-dev", "Repository": "https://biocstaging.r-universe.dev", "Date/Publication": "2026-06-09 12:03:53 UTC", "RemoteUrl": "https://github.com/BiocStaging/IntegratedLearner", "RemoteRef": "HEAD", "RemoteSha": "2952c7c8eef230756be15d59837d648871049044", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-09 13:48:29 UTC", "User": "root" }, "Author": "Nalin Arora [aut, cre, cph] (ORCID:\n),\nAnupreet Porwal [aut],\nHimel Mallick [aut]", "Maintainer": "Nalin Arora ", "MD5sum": "1a26c51aa658e588dd5e7f9ef5cc3f3e", "_user": "biocstaging", "_type": "src", "_file": "IntegratedLearner_0.99.0.tar.gz", "_fileid": "7dd2d4a85da35515b56a533a22665502916f7a4e8d5393770e74084a3f1614c4", "_filesize": 10966013, "_sha256": "7dd2d4a85da35515b56a533a22665502916f7a4e8d5393770e74084a3f1614c4", "_created": "2026-06-09T13:48:29.000Z", "_published": "2026-06-09T13:54:02.485Z", "_jobs": [ { "job": 80338815665, "time": 203, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7509726377" }, { "job": 80338815823, "time": 237, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7509742231" }, { "job": 80338815637, "time": 250, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7509747672" }, { "job": 80338815600, "time": 160, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7509762339" }, { "job": 80338815594, "time": 151, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7509757525" }, { "job": 80337501574, "time": 354, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7509631183" }, { "job": 80338815766, "time": 170, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7509711409" }, { "job": 80338815684, "time": 177, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7509714965" }, { "job": 80338815669, "time": 176, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7509713814" }, { "job": 80338815655, "time": 184, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7509718239" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 4 }, "_buildurl": "https://github.com/r-universe/biocstaging/actions/runs/27210370344", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/BiocStaging/IntegratedLearner", "_commit": { "id": "2952c7c8eef230756be15d59837d648871049044", "author": "Nalin Arora <102464913+Nalin21478@users.noreply.github.com>", "committer": "GitHub ", "message": "Delete .github/workflows directory", "time": 1781006633 }, "_maintainer": { "name": "Nalin Arora", "email": "naa4050@med.cornell.edu" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.5.0", "role": "Depends" }, { "package": "methods", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "nnet", "role": "Imports" }, { "package": "SuperLearner", "role": "Imports" }, { "package": "survival", "role": "Imports" }, { "package": "glmnet", "role": "Imports" }, { "package": "ranger", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "MultiAssayExperiment", "role": "Imports" }, { "package": "caret", "role": "Imports" }, { "package": "ROCR", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "BART", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "CoxBoost", "role": "Suggests" }, { "package": "bayesplot", "role": "Suggests" }, { "package": "bayesreg", "role": "Suggests" }, { "package": "bartMachine", "role": "Suggests" }, { "package": "cowplot", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "gbm", "role": "Suggests" }, { "package": "glmnetUtils", "role": "Suggests" }, { "package": "mlbench", "role": "Suggests" }, { "package": "mboost", "role": "Suggests" }, { "package": "nloptr", "role": "Suggests" }, { "package": "prediction", "role": "Suggests" }, { "package": "quadprog", "role": "Suggests" }, { "package": "randomForest", "role": "Suggests" }, { "package": "S4Vectors", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "timeROC", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "xgboost", "role": "Suggests" } ], "_owner": "biocstaging", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-46", "n": 1 }, { "week": "2025-47", "n": 3 }, { "week": "2026-09", "n": 1 }, { "week": "2026-11", "n": 8 }, { "week": "2026-12", "n": 10 }, { "week": "2026-13", "n": 10 }, { "week": "2026-14", "n": 5 }, { "week": "2026-16", "n": 4 }, { "week": "2026-18", "n": 3 }, { "week": "2026-19", "n": 2 }, { "week": "2026-20", "n": 1 }, { "week": "2026-21", "n": 2 }, { "week": "2026-22", "n": 6 }, { "week": "2026-24", "n": 5 } ], "_tags": [], "_topics": [ "software", "classification", "survival", "microbiome" ], "_stars": 0, "_contributors": [ { "user": "nalin21478", "count": 70, "uuid": 102464913 }, { "user": "himelmallick", "count": 9, "uuid": 18686976 }, { "user": "artur-sannikov", "count": 1, "uuid": 40318410 } ], "_userbio": { "uuid": 278472782, "type": "organization", "name": "BiocStaging" }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/IntegratedLearner" }, "_devurl": "https://github.com/himelmallick/integratedlearner", "_searchresults": 11, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/IntegratedLearner.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_cranurl": false, "_exports": [ "auc.obj", "IL_conbin", "IL_multiclass", "IL_survival", "ILsurv", "IntegratedLearner", "NNLS", "SL.BART", "SL.enet", "SL.glmnet2", "SL.horseshoe", "SL.LASSO", "SL.mxBART", "SL.nnls.auc" ], "_datasets": [ { "name": "FranzosaE_2019_CuratedMetabolome", "title": "Franzosa et al. 2019 training metabolome table", "object": "FranzosaE_2019_CuratedMetabolome", "file": "FranzosaE_2019_CuratedMetabolome.RData", "class": [ "data.frame" ], "fields": [ "X", "X4.hydroxystyrene", "p.hydroxyphenylacetate", "acesulfame", "phenyllactate", "azelate", "sebacate", "undecanedionate", "acetytyrosine", "myristic.acid", "dodecanedioic.acid", "X2.hydroxymyristic.acid", "palmitoleic.acid", "palmitic.acid", "tetradecanedioate", "X1.2.3.4.tetrahydro.b.carboline.1.3.dicarboxylic.acid", "X2.hydroxyhexadecanoate", "alpha.linolenic.acid", "linoleic.acid", "oleic.acid", "stearic.acid", "hexadecanedioic.acid", "eicosapentaenoic.acid", "arachidonic.acid", "eicosenoate", "X12.13.diHOME", "X9.10.diHOME", "docosahexaenoic.acid", "carnosol", "adrenic.acid", "palmitoylethanolamide", "X13.docosenoate", "eicosatrienoic.acid", "nervonic.acid", "docosapentaenoic.acid", "lithocholic.acid", "hyodeoxycholate.ursodeoxycholate", "deoxycholic.acid", "ketodeoxycholate", "X7.ketodeoxycholate", "alpha.muricholate", "chenodeoxycholate", "glycolithocholic.acid", "glycodeoxycholic.acid", "glycoursodeoxycholic.acid", "oleanolic.acid", "maslinic.acid", "taurolithocholic.acid", "taurochenodesoxycholic.acid", "taurodeoxycholic.acid", "taurohyodeoxycholate..tauroursodeoxycholate", "cholate", "X7.hexadecenoic.acid.methyl.ester", "piperine", "sphingosine", "stearoyl.ethanolamide", "palmitoyl.glycerol", "C16.1.MAG", "C18.0e.MAG", "N.oleoylethanolamine", "cholesterol", "C18.0.MAG", "beta.sitosterol", "C22.1.MAG", "epoxysqualene", "C24.0.TAG", "C16.0.LPC", "C20.0.LPE", "C18.3.LPC", "C18.2.LPC", "C18.0.LPC", "C16.0.ceramide..d18.1.", "C20.5.LPC", "C30.0.DAG", "C32.2.DAG", "C32.0.DAG", "C34.3.DAG", "C34.2.DAG", "C34.1.DAG", "C34.0.DAG", "C14.0.CE", "C36.4.DAG", "C36.3.DAG", "C36.2.DAG", "C16.1.CE", "C16.0.CE", "C36.0.DAG", "C18.3.CE", "C38.5.DAG", "C18.2.CE", "C18.1.CE", "linoleoyl.ethanolamide", "C18.0.CE", "C14.0.SM", "C20.4.CE", "C20.5.CE", "C20.3.CE", "C16.1.SM", "C22.5.CE", "C22.4.CE", "C22.6.CE", "C34.0.PE", "C18.0.SM", "C32.1.PC", "C42.0.TAG", "C34.1.PC.plasmalogen.A", "C34.2.PC", "C34.1.PC", "C36.5.PC.plasmalogen.A", "C36.5.PC.plasmalogen.B", "C44.1.TAG", "C44.0.TAG", "cholestenone", "C36.2.PC.plasmalogen", "C36.4.PC.A", "C36.4.PC.B", "C36.3.PC", "C22.1.SM", "C36.2.PC", "C22.0.SM", "C36.1.PC", "C46.2.TAG", "C46.1.TAG", "C46.0.TAG", "C24.1.SM", "C24.0.SM", "C48.2.TAG", "C48.4.TAG", "C48.3.TAG", "C48.0.TAG", "C48.1.TAG", "C49.1.TAG", "C50.4.TAG", "C50.3.TAG", "C50.5.TAG", "C50.1.TAG", "C50.2.TAG", "C50.0.TAG", "C51.3.TAG", "C51.2.TAG", "C52.6.TAG", "C52.5.TAG", "C52.7.TAG", "C51.0.TAG", "C52.4.TAG", "C52.3.TAG", "C52.2.TAG", "C52.1.TAG", "C52.0.TAG", "C53.3.TAG", "C54.9.TAG", "C54.6.TAG", "C54.8.TAG", "C54.5.TAG", "C54.7.TAG", "C54.4.TAG", "C54.3.TAG", "C54.2.TAG", "C54.1.TAG", "C55.3.TAG", "C55.2.TAG", "C56.6.TAG", "C56.7.TAG", "C56.4.TAG", "C56.3.TAG", "C56.5.TAG", "C56.2.TAG", "C56.1.TAG", "C58.7.TAG", "C58.6.TAG", "propionate", "butyrate...isobutytare", "alanine", "oxalate", "lactate", "methylbutyric.aid...valeric...isovaleric", "X2.aminobutyric.acid", "malonate", "alpha.hydroxybutyrate", "glycerate", "pyrocatechol", "uracil", "proline", "fumarate.maleate", "alpha.ketoisovalerate", "caproic.acid", "valine", "succite", "hydroxyisovaleric.acid", "threonine", "X4.hydroxybenzaldehyde", "nicotinate", "X4.methylcatechol", "taurine", "thymine", "acetylalanine", "X2.hydroxy.3.methylpentanoic.acid....leucinic.acid", "aspartate", "malate", "adenine", "erythronic.acid", "hypoxanthine", "phenylacetate", "salicylate", "X4.nitrophenol", "caprylic.acid", "alpha.ketoglutarate", "X2.methylglutaric.acid", "X2.hydroxyglutarate", "tartarate", "xylose", "hydrocinnamic.acid", "guanine", "xanthine", "ribitol", "dihydroxybenzoic.acid", "histidine", "orotate", "imidazolelactate", "X3.methyladipate.pimelate", "levoglucosan", "fucose", "phenylalanine", "L.phenyllactic.acid", "urate", "shikimate", "suberate", "arginine", "citrulline", "ascorbate", "fructose.glucose.galactose", "tyrosine", "homovanillate", "sorbitol", "saccharin", "X4.pyridoxate", "azelaic.acid", "N.acetylglutamate", "citrate", "glucurote", "tryptophan", "X1.3.7.trimethylurate", "pantothete", "ethyl.glucuronide", "X1.2.3.4.tetrahydro.1.methyl.beta.carboline.3.carboxylic.acid", "cystine", "pentadecanoate", "uridine", "pseudouridine", "deoxyinosine", "inosine", "heptadecanoate", "guanosine", "docosapentaenoate", "lactose", "riboflavin", "lithocholate", "chenodeoxycholate.deoxycholate", "glycocholate", "taurodeoxycholate.taurochenodeoxycholate", "putrescine", "beta.alanine", "choline", "serine", "cytosine", "histamine", "creatinine", "N.acetylputrescine", "betaine", "trimethylbenzene", "nicotinic.acid", "pyroglutamic.acid", "pipecolic.acid", "N.methylproline", "hydroxyproline", "creatine", "leucine", "isoleucine", "asparagine", "ornithine", "X1.methylnicotinamide", "trigonelline", "X2.hydroxyphenethylamine", "urocanic.acid", "imidazole.propionate", "proline.betaine", "X4.guanidinobutanoic.acid", "butyrobetaine", "acetylcholine", "glutamine", "lysine", "glutamate", "methionine", "triethanolamine", "X4.hydroxy.3.methylacetophenone", "pyridoxamine", "methylpyridonecarboxamide", "carnitine", "methionine.sulfoxide", "X1.methylguanine", "X7.methylguanine", "X3.methylxanthine", "X3.methylhistidine", "dimethyllysine", "N.acetylspermidine", "NMMA", "trimethyllysine", "kynurenic.acid", "caffeine", "N.acetylhistidine", "X5.acetylamino.6.amino.3.methyluracil", "ADMA.SDMA", "ADMA", "C2.carnitine", "N.acetylglutamic.acid", "L.1.2.3.4.tetrahydro.beta.carboline.3.carboxylic.acid", "N.acetyl.L.arginine", "pantothenate", "carnosine", "C4.carnitine", "geranyl.acetoacetate", "anserine", "X2.deoxyadenosine", "C3.DC.CH3.carnitine", "thiamine", "atenolol", "threosphingosine", "ethyl.9.hexadecenoate", "X8.hydroxy.deoxyguanosine", "diacetylspermine", "sphinganine", "phytosphingosine", "X5alpha.cholestanol", "C14.carnitine", "C16.carnitine", "C18.2.carnitine", "C18.1.carnitine", "C18.carnitine", "C20.4.carnitine", "C16.0.LPE", "C20.carnitine", "C16.1.LPC.plasmalogen", "C18.1.LPC.plasmalogen", "C18.1.LPC", "bilirubin", "urobilin", "C16.0.SM" ], "rows": 155, "table": true, "tojson": true }, { "name": "FranzosaE_2019_CuratedMetadata", "title": "Franzosa et al. 2019 training metadata", "object": "FranzosaE_2019_CuratedMetadata", "file": "FranzosaE_2019_CuratedMetadata.RData", "class": [ "data.frame" ], "fields": [ "X", "study_name", "Age", "BMI", "seq_type", "country", "Gender", "age_category", "body_site", "diseaseCat", "cohort_life_style", "MetabolomicsType", "Metabolomics_body_site", "Subject_ID", "diseaseCat_clean", "longitudinal", "sample_id" ], "rows": 155, "table": true, "tojson": true }, { "name": "FranzosaE_2019_CuratedSpeciesProfile", "title": "Franzosa et al. 2019 training species profile", "object": "FranzosaE_2019_CuratedSpeciesProfile", "file": "FranzosaE_2019_CuratedSpeciesProfile.RData", "class": [ "data.frame" ], "fields": [ "X", "Abiotrophia_defectiva", "Abiotrophia_sp_HMSC24B09", "Absiella_dolichum", "Acetobacter_sp_CAG_267", "Acidaminococcus_fermentans", "Acidaminococcus_intestini", "Acinetobacter_johnsonii", "Actinobaculum_massiliense", "Actinobaculum_sp_oral_taxon_183", "Actinomyces_georgiae", "Actinomyces_graevenitzii", "Actinomyces_hongkongensis", "Actinomyces_johnsonii", "Actinomyces_massiliensis", "Actinomyces_meyeri", "Actinomyces_naeslundii", "Actinomyces_odontolyticus", "Actinomyces_oris", "Actinomyces_radicidentis", "Actinomyces_sp_HMSC035G02", "Actinomyces_sp_HPA0247", "Actinomyces_sp_ICM47", "Actinomyces_sp_S6_Spd3", "Actinomyces_sp_oral_taxon_170", "Actinomyces_sp_oral_taxon_180", "Actinomyces_sp_oral_taxon_181", "Actinomyces_sp_oral_taxon_414", "Actinomyces_sp_oral_taxon_448", "Actinomyces_turicensis", "Actinomyces_viscosus", "Adlercreutzia_equolifaciens", "Agathobaculum_butyriciproducens", "Aggregatibacter_aphrophilus", "Aggregatibacter_segnis", "Akkermansia_muciniphila", "Alistipes_finegoldii", "Alistipes_indistinctus", "Alistipes_inops", "Alistipes_obesi", "Alistipes_onderdonkii", "Alistipes_putredinis", "Alistipes_shahii", "Alistipes_sp_58_9_plus", "Alistipes_sp_An31A", "Alistipes_sp_CAG_268", "Alistipes_sp_CHKCI003", "Alistipes_timonensis", "Allisonella_histaminiformans", "Alloscardovia_omnicolens", "Anaerococcus_lactolyticus", "Anaerococcus_vaginalis", "Anaerofilum_sp_An201", "Anaerofustis_stercorihominis", "Anaeroglobus_geminatus", "Anaeromassilibacillus_sp_An250", "Anaerostipes_caccae", "Anaerostipes_hadrus", "Anaerotignum_lactatifermentans", "Anaerotruncus_colihominis", "Anaerotruncus_sp_CAG_528", "Arthrospira_platensis", "Asaccharobacter_celatus", "Atopobium_deltae", "Atopobium_minutum", "Atopobium_parvulum", "Atopobium_rimae", "Atopobium_vaginae", "Azospirillum_sp_47_25", "Azospirillum_sp_CAG_260", "Bacillus_coagulans", "Bacteroides_caccae", "Bacteroides_cellulosilyticus", "Bacteroides_clarus", "Bacteroides_coagulans", "Bacteroides_coprocola", "Bacteroides_coprophilus", "Bacteroides_dorei", "Bacteroides_eggerthii", "Bacteroides_faecis", "Bacteroides_finegoldii", "Bacteroides_fluxus", "Bacteroides_fragilis", "Bacteroides_galacturonicus", "Bacteroides_intestinalis", "Bacteroides_massiliensis", "Bacteroides_nordii", "Bacteroides_ovatus", "Bacteroides_pectinophilus", "Bacteroides_plebeius", "Bacteroides_salyersiae", "Bacteroides_sartorii", "Bacteroides_sp_CAG_1060", "Bacteroides_sp_CAG_1076", "Bacteroides_sp_CAG_144", "Bacteroides_sp_CAG_443", "Bacteroides_sp_CAG_530", "Bacteroides_sp_CAG_545", "Bacteroides_sp_CAG_598", "Bacteroides_sp_CAG_661", "Bacteroides_sp_CAG_709", "Bacteroides_sp_CAG_754", "Bacteroides_sp_CAG_770", "Bacteroides_sp_CAG_875", "Bacteroides_sp_CAG_927", "Bacteroides_sp_D2", "Bacteroides_sp_OM08_11", "Bacteroides_stercorirosoris", "Bacteroides_stercoris", "Bacteroides_thetaiotaomicron", "Bacteroides_uniformis", "Bacteroides_vulgatus", "Bacteroides_xylanisolvens", "Barnesiella_intestinihominis", "Barnesiella_sp_An22", "Barnesiella_viscericola", "Bifidobacterium_adolescentis", "Bifidobacterium_angulatum", "Bifidobacterium_animalis", "Bifidobacterium_bifidum", "Bifidobacterium_breve", "Bifidobacterium_catenulatum", "Bifidobacterium_dentium", "Bifidobacterium_gallinarum", "Bifidobacterium_kashiwanohense", "Bifidobacterium_longum", "Bifidobacterium_pseudocatenulatum", "Bifidobacterium_pseudolongum", "Bifidobacterium_pullorum", "Bifidobacterium_saeculare", "Bifidobacterium_scardovii", "Bilophila_wadsworthia", "Blastocystis_sp_subtype_1", "Blautia_coccoides", "Blautia_hansenii", "Blautia_hydrogenotrophica", "Blautia_obeum", "Blautia_producta", "Blautia_sp", "Blautia_sp_AF19_10LB", "Blautia_sp_An249", "Blautia_sp_CAG_257", "Blautia_sp_CAG_52", "Blautia_sp_N6H1_15", "Blautia_wexlerae", "Brochothrix_thermosphacta", "Bulleidia_extructa", "Butyribacterium_methylotrophicum", "Butyricicoccus_porcorum", "Butyricicoccus_pullicaecorum", "Butyricimonas_sp", "Butyricimonas_synergistica", "Butyricimonas_virosa", "Butyrivibrio_crossotus", "Butyrivibrio_sp_CAG_318", "Campylobacter_concisus", "Campylobacter_curvus", "Campylobacter_gracilis", "Campylobacter_hominis", "Campylobacter_showae", "Campylobacter_ureolyticus", "Candidatus_Gastranaerophilales_bacterium", "Candidatus_Gastranaerophilales_bacterium_HUM_10", "Candidatus_Gastranaerophilales_bacterium_HUM_11", "Candidatus_Gastranaerophilales_bacterium_HUM_18", "Candidatus_Gastranaerophilales_bacterium_HUM_21", "Candidatus_Melainabacteria_bacterium_35_41", "Candidatus_Methanomassiliicoccus_intestinalis", "Candidatus_Saccharibacteria_oral_taxon_TM7x", "Candidatus_Stoquefichus_sp_KLE1796", "Cardiobacterium_hominis", "Carnobacterium_divergens", "Carnobacterium_maltaromaticum", "Catabacter_hongkongensis", "Catenibacterium_mitsuokai", "Cetobacterium_somerae", "Christensenella_minuta", "Chryseobacterium_bovis", "Citrobacter_amalonaticus", "Citrobacter_braakii", "Citrobacter_europaeus", "Citrobacter_farmeri", "Citrobacter_freundii", "Citrobacter_koseri", "Citrobacter_portucalensis", "Citrobacter_werkmanii", "Cloacibacillus_evryensis", "Cloacibacillus_porcorum", "Clostridiales_Family_XIII_bacterium", "Clostridiales_bacterium_1_7_47FAA", "Clostridiales_bacterium_CHKCI006", "Clostridiales_bacterium_KA00274", "Clostridiales_bacterium_KLE1615", "Clostridiales_bacterium_S5_A14a", "Clostridioides_difficile", "Clostridium_aldenense", "Clostridium_asparagiforme", "Clostridium_baratii", "Clostridium_bolteae", "Clostridium_butyricum", "Clostridium_cadaveris", "Clostridium_celatum", "Clostridium_citroniae", "Clostridium_clostridioforme", "Clostridium_colicanis", "Clostridium_disporicum", "Clostridium_hiranonis", "Clostridium_hylemonae", "Clostridium_innocuum", "Clostridium_lavalense", "Clostridium_leptum", "Clostridium_methylpentosum", "Clostridium_neonatale", "Clostridium_paraputrificum", "Clostridium_perfringens", "Clostridium_saccharolyticum", "Clostridium_scindens", "Clostridium_sp_44_14", "Clostridium_sp_7_2_43FAA", "Clostridium_sp_AF36_4", "Clostridium_sp_AM22_11AC", "Clostridium_sp_AM58_1XD", "Clostridium_sp_CAG_1193", "Clostridium_sp_CAG_122", "Clostridium_sp_CAG_12237_41", "Clostridium_sp_CAG_138", "Clostridium_sp_CAG_167", "Clostridium_sp_CAG_169", "Clostridium_sp_CAG_217", "Clostridium_sp_CAG_221", "Clostridium_sp_CAG_226", "Clostridium_sp_CAG_230", "Clostridium_sp_CAG_242", "Clostridium_sp_CAG_245", "Clostridium_sp_CAG_253", "Clostridium_sp_CAG_265", "Clostridium_sp_CAG_269", "Clostridium_sp_CAG_273", "Clostridium_sp_CAG_277", "Clostridium_sp_CAG_288", "Clostridium_sp_CAG_299", "Clostridium_sp_CAG_302", "Clostridium_sp_CAG_306", "Clostridium_sp_CAG_307", "Clostridium_sp_CAG_349", "Clostridium_sp_CAG_354", "Clostridium_sp_CAG_356", "Clostridium_sp_CAG_389", "Clostridium_sp_CAG_411", "Clostridium_sp_CAG_413", "Clostridium_sp_CAG_417", "Clostridium_sp_CAG_433", "Clostridium_sp_CAG_440", "Clostridium_sp_CAG_448", "Clostridium_sp_CAG_451", "Clostridium_sp_CAG_452", "Clostridium_sp_CAG_465", "Clostridium_sp_CAG_470", "Clostridium_sp_CAG_492", "Clostridium_sp_CAG_505", "Clostridium_sp_CAG_508", "Clostridium_sp_CAG_533", "Clostridium_sp_CAG_557", "Clostridium_sp_CAG_567", "Clostridium_sp_CAG_571", "Clostridium_sp_CAG_575", "Clostridium_sp_CAG_58", "Clostridium_sp_CAG_590", "Clostridium_sp_CAG_594", "Clostridium_sp_CAG_628", "Clostridium_sp_CAG_678", "Clostridium_sp_CAG_710", "Clostridium_sp_CAG_75", "Clostridium_sp_CAG_762", "Clostridium_sp_CAG_768", "Clostridium_sp_CAG_780", "Clostridium_sp_CAG_793", "Clostridium_sp_CAG_798", "Clostridium_sp_CAG_914", "Clostridium_sp_CAG_921", "Clostridium_sp_D5", "Clostridium_sp_MSTE9", "Clostridium_sp_chh4_2", "Clostridium_spiroforme", "Clostridium_symbiosum", "Clostridium_thermobutyricum", "Clostridium_ventriculi", "Collinsella_aerofaciens", "Collinsella_intestinalis", "Collinsella_massiliensis", "Collinsella_sp", "Collinsella_sp_An7", "Collinsella_sp_CAG_289", "Collinsella_stercoris", "Collinsella_tanakaei", "Coprobacillus_cateniformis", "Coprobacillus_sp_CAG_605", "Coprobacillus_sp_CAG_698", "Coprobacter_fastidiosus", "Coprobacter_secundus", "Coprobacter_sp", "Coprococcus_catus", "Coprococcus_comes", "Coprococcus_eutactus", "Coraliomargarita_sp_CAG_312", "Corallococcus_sp_CAG_1435", "Corynebacterium_amycolatum", "Corynebacterium_argentoratense", "Corynebacterium_durum", "Corynebacterium_glutamicum", "Corynebacterium_matruchotii", "Corynebacterium_striatum", "Cryptobacterium_sp_CAG_338", "Desulfovibrio_desulfuricans", "Desulfovibrio_fairfieldensis", "Desulfovibrio_piger", "Desulfovibrio_sp_AM18_2", "Desulfovibrionaceae_bacterium", "Dialister_invisus", "Dialister_micraerophilus", "Dialister_pneumosintes", "Dialister_sp_CAG_357", "Dialister_sp_CAG_486", "Dialister_succinatiphilus", "Dielma_fastidiosa", "Dorea_formicigenerans", "Dorea_longicatena", "Dorea_sp_CAG_317", "Dorea_sp_OM02_2LB", "Eggerthella_lenta", "Eggerthella_sinensis", "Eggerthella_sp_CAG_1427", "Eggerthella_sp_CAG_209", "Eggerthella_sp_CAG_298", "Eggerthella_sp_CAG_368", "Eggerthella_sp_YY7918", "Eikenella_corrodens", "Eisenbergiella_massiliensis", "Eisenbergiella_tayi", "Enorma_massiliensis", "Enterobacter_bugandensis", "Enterobacter_cloacae_complex", "Enterobacter_soli", "Enterococcus_avium", "Enterococcus_canintestini", "Enterococcus_casseliflavus", "Enterococcus_durans", "Enterococcus_faecalis", "Enterococcus_faecium", "Enterococcus_gallinarum", "Enterococcus_hirae", "Enterococcus_phoeniculicola", "Enterococcus_raffinosus", "Enterococcus_thailandicus", "Enterorhabdus_caecimuris", "Enteroscipio_rubneri", "Erysipelatoclostridium_ramosum", "Erysipelotrichaceae_bacterium_3_1_53", "Escherichia_coli", "Eubacteriaceae_bacterium_CHKCI005", "Eubacterium_brachy", "Eubacterium_callanderi", "Eubacterium_coprostanoligenes", "Eubacterium_eligens", "Eubacterium_hallii", "Eubacterium_limosum", "Eubacterium_maltosivorans", "Eubacterium_pyruvativorans", "Eubacterium_ramulus", "Eubacterium_rectale", "Eubacterium_siraeum", "Eubacterium_sp_36_13", "Eubacterium_sp_AF17_7", "Eubacterium_sp_AM18_10LB_B", "Eubacterium_sp_An11", "Eubacterium_sp_CAG_115", "Eubacterium_sp_CAG_161", "Eubacterium_sp_CAG_180", "Eubacterium_sp_CAG_192", "Eubacterium_sp_CAG_251", "Eubacterium_sp_CAG_252", "Eubacterium_sp_CAG_274", "Eubacterium_sp_CAG_38", "Eubacterium_sp_CAG_581", "Eubacterium_sp_CAG_841", "Eubacterium_sp_OM08_24", "Eubacterium_sp_TM05_53", "Eubacterium_sulci", "Eubacterium_ventriosum", "Faecalibacterium_prausnitzii", "Faecalibacterium_sp_CAG_74", "Faecalibacterium_sp_CAG_74_58_120", "Faecalicatena_orotica", "Faecalicoccus_pleomorphus", "Faecalitalea_cylindroides", "Finegoldia_magna", "Firmicutes_bacterium_AF16_15", "Firmicutes_bacterium_AM10_47", "Firmicutes_bacterium_CAG_102", "Firmicutes_bacterium_CAG_103", "Firmicutes_bacterium_CAG_110", "Firmicutes_bacterium_CAG_114", "Firmicutes_bacterium_CAG_124", "Firmicutes_bacterium_CAG_129", "Firmicutes_bacterium_CAG_137", "Firmicutes_bacterium_CAG_145", "Firmicutes_bacterium_CAG_170", "Firmicutes_bacterium_CAG_176", "Firmicutes_bacterium_CAG_194", "Firmicutes_bacterium_CAG_238", "Firmicutes_bacterium_CAG_240", "Firmicutes_bacterium_CAG_24053_14", "Firmicutes_bacterium_CAG_272", "Firmicutes_bacterium_CAG_313", "Firmicutes_bacterium_CAG_321", "Firmicutes_bacterium_CAG_345", "Firmicutes_bacterium_CAG_41", "Firmicutes_bacterium_CAG_424", "Firmicutes_bacterium_CAG_449", "Firmicutes_bacterium_CAG_460", "Firmicutes_bacterium_CAG_466", "Firmicutes_bacterium_CAG_475", "Firmicutes_bacterium_CAG_534", "Firmicutes_bacterium_CAG_555", "Firmicutes_bacterium_CAG_56", "Firmicutes_bacterium_CAG_582", "Firmicutes_bacterium_CAG_631", "Firmicutes_bacterium_CAG_646", "Firmicutes_bacterium_CAG_65_45_313", "Firmicutes_bacterium_CAG_83", "Firmicutes_bacterium_CAG_882", "Firmicutes_bacterium_CAG_94", "Firmicutes_bacterium_CAG_95", "Flavonifractor_plautii", "Flavonifractor_sp_An10", "Flavonifractor_sp_An100", "Fusicatenibacter_saccharivorans", "Fusobacterium_equinum", "Fusobacterium_gonidiaformans", "Fusobacterium_nucleatum", "Fusobacterium_periodonticum", "Fusobacterium_sp_CAG_439", "Fusobacterium_ulcerans", "Fusobacterium_varium", "Gardnerella_vaginalis", "Gemella_bergeri", "Gemella_haemolysans", "Gemella_morbillorum", "Gemella_sanguinis", "Gemmiger_formicilis", "Gemmiger_sp_An50", "Gemmiger_sp_An87", "Gordonibacter_pamelaeae", "Gordonibacter_sp_An232A", "Gordonibacter_urolithinfaciens", "Granulicatella_adiacens", "Haemophilus_haemolyticus", "Haemophilus_parainfluenzae", "Haemophilus_pittmaniae", "Haemophilus_sp_HMSC71H05", "Haemophilus_sputorum", "Hafnia_alvei", "Hafnia_paralvei", "Harryflintia_acetispora", "Holdemanella_biformis", "Holdemania_filiformis", "Hungatella_hathewayi", "Intestinibacter_bartlettii", "Intestinimonas_butyriciproducens", "Kingella_oralis", "Klebsiella_aerogenes", "Klebsiella_michiganensis", "Klebsiella_oxytoca", "Klebsiella_pneumoniae", "Klebsiella_quasipneumoniae", "Klebsiella_variicola", "Kluyvera_cryocrescens", "Kluyvera_intestini", "Kosakonia_pseudosacchari", "Kosakonia_sp_S29", "Lachnoanaerobaculum_saburreum", "Lachnoclostridium_sp_An118", "Lachnoclostridium_sp_An131", "Lachnoclostridium_sp_An138", "Lachnoclostridium_sp_An14", "Lachnoclostridium_sp_An169", "Lachnoclostridium_sp_An181", "Lachnoclostridium_sp_An196", "Lachnoclostridium_sp_An76", "Lachnospira_pectinoschiza", "Lachnospiraceae_bacterium_2_1_46FAA", "Lachnospiraceae_bacterium_OF09_33XD", "Lachnospiraceae_bacterium_OF09_6", "Lachnospiraceae_bacterium_oral_taxon_096", "Lactobacillus_acidophilus", "Lactobacillus_agilis", "Lactobacillus_algidus", "Lactobacillus_amylovorus", "Lactobacillus_animalis", "Lactobacillus_antri", "Lactobacillus_apis", "Lactobacillus_casei_group", "Lactobacillus_crispatus", "Lactobacillus_curvatus", "Lactobacillus_delbrueckii", "Lactobacillus_equicursoris", "Lactobacillus_fermentum", "Lactobacillus_gasseri", "Lactobacillus_helveticus", "Lactobacillus_iners", "Lactobacillus_jensenii", "Lactobacillus_johnsonii", "Lactobacillus_kalixensis", "Lactobacillus_kullabergensis", "Lactobacillus_mucosae", "Lactobacillus_oris", "Lactobacillus_pantheris", "Lactobacillus_paragasseri", "Lactobacillus_pentosus", "Lactobacillus_plantarum", "Lactobacillus_pontis", "Lactobacillus_reuteri", "Lactobacillus_rhamnosus", "Lactobacillus_rogosae", "Lactobacillus_ruminis", "Lactobacillus_saerimneri", "Lactobacillus_sakei", "Lactobacillus_salivarius", "Lactobacillus_ultunensis", "Lactobacillus_vaccinostercus", "Lactobacillus_vaginalis", "Lactococcus_lactis", "Lactococcus_piscium", "Lactococcus_plantarum", "Lactococcus_raffinolactis", "Lactonifactor_longoviformis", "Lawsonella_clevelandensis", "Lawsonibacter_asaccharolyticus", "Lentisphaerae_bacterium", "Leptotrichia_hofstadii", "Leptotrichia_wadei", "Leuconostoc_carnosum", "Leuconostoc_citreum", "Leuconostoc_garlicum", "Leuconostoc_gelidum", "Leuconostoc_lactis", "Leuconostoc_mesenteroides", "Leuconostoc_pseudomesenteroides", "Marvinbryantia_formatexigens", "Massiliomicrobiota_timonensis", "Mediterraneibacter_sp_KCTC_15684", "Megamonas_funiformis", "Megasphaera_elsdenii", "Megasphaera_hexanoica", "Megasphaera_micronuciformis", "Megasphaera_sp_DISK_18", "Megasphaera_sp_MJR8396C", "Mesosutterella_multiformis", "Methanobrevibacter_arboriphilus", "Methanobrevibacter_smithii", "Methanosphaera_stadtmanae", "Microvirgula_aerodenitrificans", "Mitsuokella_jalaludinii", "Mogibacterium_diversum", "Mogibacterium_pumilum", "Mogibacterium_timidum", "Monoglobus_pectinilyticus", "Moraxella_osloensis", "Morganella_morganii", "Murimonas_intestini", "Mycoplasma_sp_CAG_472", "Mycoplasma_sp_CAG_877", "Negativicoccus_succinicivorans", "Neisseria_bacilliformis", "Neisseria_flavescens", "Neisseria_subflava", "Odoribacter_laneus", "Odoribacter_splanchnicus", "Olsenella_profusa", "Olsenella_uli", "Oribacterium_parvum", "Oribacterium_sinus", "Oribacterium_sp_oral_taxon_078", "Oscillibacter_sp_57_20", "Oscillibacter_sp_CAG_155", "Oscillibacter_sp_CAG_241", "Oscillibacter_sp_PC13", "Oxalobacter_formigenes", "Parabacteroides_distasonis", "Parabacteroides_goldsteinii", "Parabacteroides_gordonii", "Parabacteroides_johnsonii", "Parabacteroides_merdae", "Parabacteroides_sp_CAG_409", "Paraeggerthella_hongkongensis", "Paraprevotella_clara", "Paraprevotella_xylaniphila", "Parascardovia_denticolens", "Parasutterella_excrementihominis", "Parvimonas_micra", "Parvimonas_sp_KA00067", "Parvimonas_sp_oral_taxon_110", "Pediococcus_acidilactici", "Pediococcus_pentosaceus", "Pedobacter_himalayensis", "Peptococcus_niger", "Peptoniphilus_coxii", "Peptoniphilus_duerdenii", "Peptoniphilus_harei", "Peptoniphilus_lacrimalis", "Peptoniphilus_sp_HMSC062D09", "Peptoniphilus_sp_oral_taxon_375", "Peptostreptococcaceae_bacterium_oral_taxon_929", "Peptostreptococcus_anaerobius", "Peptostreptococcus_sp_MV1", "Peptostreptococcus_stomatis", "Phascolarctobacterium_faecium", "Phascolarctobacterium_sp_CAG_266", "Phascolarctobacterium_succinatutens", "Porphyromonas_asaccharolytica", "Porphyromonas_sp_31_2", "Porphyromonas_sp_HMSC065F10", "Porphyromonas_uenonis", "Prevotella_bivia", "Prevotella_buccae", "Prevotella_buccalis", "Prevotella_copri", "Prevotella_corporis", "Prevotella_denticola", "Prevotella_disiens", "Prevotella_sp_109", "Prevotella_sp_885", "Prevotella_sp_CAG_1031", "Prevotella_sp_CAG_1185", "Prevotella_sp_CAG_279", "Prevotella_sp_CAG_386", "Prevotella_sp_CAG_485", "Prevotella_sp_CAG_487", "Prevotella_sp_CAG_520", "Prevotella_sp_CAG_604", "Prevotella_sp_CAG_617", "Prevotella_sp_CAG_732", "Prevotella_sp_CAG_873", "Prevotella_sp_CAG_891", "Prevotella_stercorea", "Prevotella_timonensis", "Propionibacterium_acidifaciens", "Propionibacterium_freudenreichii", "Proteobacteria_bacterium_CAG_139", "Proteobacteria_bacterium_CAG_495", "Proteus_mirabilis", "Proteus_vulgaris", "Providencia_rettgeri", "Pseudoflavonifractor_capillosus", "Pseudoflavonifractor_sp_An184", "Pseudomonas_aeruginosa_group", "Pseudomonas_fragi", "Pseudomonas_helleri", "Pseudopropionibacterium_propionicum", "Pseudoramibacter_alactolyticus", "Pyramidobacter_piscolens", "Raoultella_ornithinolytica", "Robinsoniella_sp_RHS", "Romboutsia_ilealis", "Roseburia_faecis", "Roseburia_hominis", "Roseburia_intestinalis", "Roseburia_inulinivorans", "Roseburia_sp_CAG_100", "Roseburia_sp_CAG_10041_57", "Roseburia_sp_CAG_182", "Roseburia_sp_CAG_197", "Roseburia_sp_CAG_303", "Roseburia_sp_CAG_309", "Roseburia_sp_CAG_380", "Roseburia_sp_CAG_471", "Rothia_dentocariosa", "Rothia_mucilaginosa", "Rubneribacter_badeniensis", "Ruminococcaceae_bacterium_D16", "Ruminococcaceae_bacterium_D5", "Ruminococcaceae_bacterium_KLE1738", "Ruminococcus_bicirculans", "Ruminococcus_bromii", "Ruminococcus_callidus", "Ruminococcus_champanellensis", "Ruminococcus_gnavus", "Ruminococcus_lactaris", "Ruminococcus_sp_37_24", "Ruminococcus_sp_AF31_8BH", "Ruminococcus_sp_CAG_177", "Ruminococcus_sp_CAG_254", "Ruminococcus_sp_CAG_330", "Ruminococcus_sp_CAG_353", "Ruminococcus_sp_CAG_382", "Ruminococcus_sp_CAG_403", "Ruminococcus_sp_CAG_488", "Ruminococcus_sp_CAG_563", "Ruminococcus_sp_CAG_579", "Ruminococcus_sp_CAG_624", "Ruminococcus_sp_CAG_724", "Ruminococcus_torques", "Ruthenibacterium_lactatiformans", "Saccharomyces_cerevisiae", "Sanguibacteroides_justesenii", "Scardovia_wiggsiae", "Selenomonas_artemidis", "Selenomonas_noxia", "Sellimonas_intestinalis", "Senegalimassilia_anaerobia", "Sharpea_azabuensis", "Slackia_exigua", "Slackia_isoflavoniconvertens", "Slackia_piriformis", "Solobacterium_moorei", "Staphylococcus_aureus", "Staphylococcus_epidermidis", "Stomatobaculum_longum", "Streptococcus_agalactiae", "Streptococcus_anginosus_group", "Streptococcus_australis", "Streptococcus_cristatus", "Streptococcus_downei", "Streptococcus_gallolyticus", "Streptococcus_gordonii", "Streptococcus_infantarius", "Streptococcus_infantis", "Streptococcus_lutetiensis", "Streptococcus_macedonicus", "Streptococcus_milleri", "Streptococcus_mitis", "Streptococcus_mutans", "Streptococcus_oralis", "Streptococcus_parasanguinis", "Streptococcus_pasteurianus", "Streptococcus_peroris", "Streptococcus_pneumoniae", "Streptococcus_pseudopneumoniae", "Streptococcus_salivarius", "Streptococcus_sanguinis", "Streptococcus_sobrinus", "Streptococcus_sp_A12", "Streptococcus_sp_F0442", "Streptococcus_sp_HMSC070B10", "Streptococcus_sp_HMSC071D03", "Streptococcus_sp_HPH0090", "Streptococcus_sp_UMB1385", "Streptococcus_thermophilus", "Streptococcus_vestibularis", "Subdoligranulum_sp", "Subdoligranulum_sp_APC924_74", "Sutterella_parvirubra", "Sutterella_sp_CAG_351", "Sutterella_sp_CAG_397", "Sutterella_sp_CAG_521", "Sutterella_wadsworthensis", "Terrisporobacter_othiniensis", "Turicibacter_sanguinis", "Turicimonas_muris", "Tyzzerella_nexilis", "Tyzzerella_sp", "Varibaculum_cambriense", "Veillonella_atypica", "Veillonella_dispar", "Veillonella_infantium", "Veillonella_parvula", "Veillonella_rogosae", "Veillonella_seminalis", "Veillonella_sp_CAG_933", "Veillonella_sp_DORA_A_3_16_22", "Veillonella_sp_T11011_6", "Veillonella_tobetsuensis", "Victivallales_bacterium_CCUG_44730", "Victivallis_vadensis", "Weissella_cibaria", "Weissella_confusa", "Weissella_koreensis", "Weissella_viridescens" ], "rows": 155, "table": true, "tojson": true }, { "name": "FranzosaE_2019_Validation_CuratedMetabolome", "title": "Franzosa et al. 2019 validation metabolome table", "object": "FranzosaE_2019_Validation_CuratedMetabolome", "file": "FranzosaE_2019_Validation_CuratedMetabolome.RData", "class": [ "data.frame" ], "fields": [ "X", "X4.hydroxystyrene", "p.hydroxyphenylacetate", "acesulfame", "phenyllactate", "azelate", "sebacate", "undecanedionate", "acetytyrosine", "myristic.acid", "dodecanedioic.acid", "X2.hydroxymyristic.acid", "palmitoleic.acid", "palmitic.acid", "tetradecanedioate", "X1.2.3.4.tetrahydro.b.carboline.1.3.dicarboxylic.acid", "X2.hydroxyhexadecanoate", "alpha.linolenic.acid", "linoleic.acid", "oleic.acid", "stearic.acid", "hexadecanedioic.acid", "eicosapentaenoic.acid", "arachidonic.acid", "eicosenoate", "X12.13.diHOME", "X9.10.diHOME", "docosahexaenoic.acid", "carnosol", "adrenic.acid", "palmitoylethanolamide", "X13.docosenoate", "eicosatrienoic.acid", "nervonic.acid", "docosapentaenoic.acid", "lithocholic.acid", "hyodeoxycholate.ursodeoxycholate", "deoxycholic.acid", "ketodeoxycholate", "X7.ketodeoxycholate", "alpha.muricholate", "chenodeoxycholate", "glycolithocholic.acid", "glycodeoxycholic.acid", "glycoursodeoxycholic.acid", "oleanolic.acid", "maslinic.acid", "taurolithocholic.acid", "taurochenodesoxycholic.acid", "taurodeoxycholic.acid", "taurohyodeoxycholate..tauroursodeoxycholate", "cholate", "X7.hexadecenoic.acid.methyl.ester", "piperine", "sphingosine", "stearoyl.ethanolamide", "palmitoyl.glycerol", "C16.1.MAG", "C18.0e.MAG", "N.oleoylethanolamine", "cholesterol", "C18.0.MAG", "beta.sitosterol", "C22.1.MAG", "epoxysqualene", "C24.0.TAG", "C16.0.LPC", "C20.0.LPE", "C18.3.LPC", "C18.2.LPC", "C18.0.LPC", "C16.0.ceramide..d18.1.", "C20.5.LPC", "C30.0.DAG", "C32.2.DAG", "C32.0.DAG", "C34.3.DAG", "C34.2.DAG", "C34.1.DAG", "C34.0.DAG", "C14.0.CE", "C36.4.DAG", "C36.3.DAG", "C36.2.DAG", "C16.1.CE", "C16.0.CE", "C36.0.DAG", "C18.3.CE", "C38.5.DAG", "C18.2.CE", "C18.1.CE", "linoleoyl.ethanolamide", "C18.0.CE", "C14.0.SM", "C20.4.CE", "C20.5.CE", "C20.3.CE", "C16.1.SM", "C22.5.CE", "C22.4.CE", "C22.6.CE", "C34.0.PE", "C18.0.SM", "C32.1.PC", "C42.0.TAG", "C34.1.PC.plasmalogen.A", "C34.2.PC", "C34.1.PC", "C36.5.PC.plasmalogen.A", "C36.5.PC.plasmalogen.B", "C44.1.TAG", "C44.0.TAG", "cholestenone", "C36.2.PC.plasmalogen", "C36.4.PC.A", "C36.4.PC.B", "C36.3.PC", "C22.1.SM", "C36.2.PC", "C22.0.SM", "C36.1.PC", "C46.2.TAG", "C46.1.TAG", "C46.0.TAG", "C24.1.SM", "C24.0.SM", "C48.2.TAG", "C48.4.TAG", "C48.3.TAG", "C48.0.TAG", "C48.1.TAG", "C49.1.TAG", "C50.4.TAG", "C50.3.TAG", "C50.5.TAG", "C50.1.TAG", "C50.2.TAG", "C50.0.TAG", "C51.3.TAG", "C51.2.TAG", "C52.6.TAG", "C52.5.TAG", "C52.7.TAG", "C51.0.TAG", "C52.4.TAG", "C52.3.TAG", "C52.2.TAG", "C52.1.TAG", "C52.0.TAG", "C53.3.TAG", "C54.9.TAG", "C54.6.TAG", "C54.8.TAG", "C54.5.TAG", "C54.7.TAG", "C54.4.TAG", "C54.3.TAG", "C54.2.TAG", "C54.1.TAG", "C55.3.TAG", "C55.2.TAG", "C56.6.TAG", "C56.7.TAG", "C56.4.TAG", "C56.3.TAG", "C56.5.TAG", "C56.2.TAG", "C56.1.TAG", "C58.7.TAG", "C58.6.TAG", "propionate", "butyrate...isobutytare", "alanine", "oxalate", "lactate", "methylbutyric.aid...valeric...isovaleric", "X2.aminobutyric.acid", "malonate", "alpha.hydroxybutyrate", "glycerate", "pyrocatechol", "uracil", "proline", "fumarate.maleate", "alpha.ketoisovalerate", "caproic.acid", "valine", "succite", "hydroxyisovaleric.acid", "threonine", "X4.hydroxybenzaldehyde", "nicotinate", "X4.methylcatechol", "taurine", "thymine", "acetylalanine", "X2.hydroxy.3.methylpentanoic.acid....leucinic.acid", "aspartate", "malate", "adenine", "erythronic.acid", "hypoxanthine", "phenylacetate", "salicylate", "X4.nitrophenol", "caprylic.acid", "alpha.ketoglutarate", "X2.methylglutaric.acid", "X2.hydroxyglutarate", "tartarate", "xylose", "hydrocinnamic.acid", "guanine", "xanthine", "ribitol", "dihydroxybenzoic.acid", "histidine", "orotate", "imidazolelactate", "X3.methyladipate.pimelate", "levoglucosan", "fucose", "phenylalanine", "L.phenyllactic.acid", "urate", "shikimate", "suberate", "arginine", "citrulline", "ascorbate", "fructose.glucose.galactose", "tyrosine", "homovanillate", "sorbitol", "saccharin", "X4.pyridoxate", "azelaic.acid", "N.acetylglutamate", "citrate", "glucurote", "tryptophan", "X1.3.7.trimethylurate", "pantothete", "ethyl.glucuronide", "X1.2.3.4.tetrahydro.1.methyl.beta.carboline.3.carboxylic.acid", "cystine", "pentadecanoate", "uridine", "pseudouridine", "deoxyinosine", "inosine", "heptadecanoate", "guanosine", "docosapentaenoate", "lactose", "riboflavin", "lithocholate", "chenodeoxycholate.deoxycholate", "glycocholate", "taurodeoxycholate.taurochenodeoxycholate", "putrescine", "beta.alanine", "choline", "serine", "cytosine", "histamine", "creatinine", "N.acetylputrescine", "betaine", "trimethylbenzene", "nicotinic.acid", "pyroglutamic.acid", "pipecolic.acid", "N.methylproline", "hydroxyproline", "creatine", "leucine", "isoleucine", "asparagine", "ornithine", "X1.methylnicotinamide", "trigonelline", "X2.hydroxyphenethylamine", "urocanic.acid", "imidazole.propionate", "proline.betaine", "X4.guanidinobutanoic.acid", "butyrobetaine", "acetylcholine", "glutamine", "lysine", "glutamate", "methionine", "triethanolamine", "X4.hydroxy.3.methylacetophenone", "pyridoxamine", "methylpyridonecarboxamide", "carnitine", "methionine.sulfoxide", "X1.methylguanine", "X7.methylguanine", "X3.methylxanthine", "X3.methylhistidine", "dimethyllysine", "N.acetylspermidine", "NMMA", "trimethyllysine", "kynurenic.acid", "caffeine", "N.acetylhistidine", "X5.acetylamino.6.amino.3.methyluracil", "ADMA.SDMA", "ADMA", "C2.carnitine", "N.acetylglutamic.acid", "L.1.2.3.4.tetrahydro.beta.carboline.3.carboxylic.acid", "N.acetyl.L.arginine", "pantothenate", "carnosine", "C4.carnitine", "geranyl.acetoacetate", "anserine", "X2.deoxyadenosine", "C3.DC.CH3.carnitine", "thiamine", "atenolol", "threosphingosine", "ethyl.9.hexadecenoate", "X8.hydroxy.deoxyguanosine", "diacetylspermine", "sphinganine", "phytosphingosine", "X5alpha.cholestanol", "C14.carnitine", "C16.carnitine", "C18.2.carnitine", "C18.1.carnitine", "C18.carnitine", "C20.4.carnitine", "C16.0.LPE", "C20.carnitine", "C16.1.LPC.plasmalogen", "C18.1.LPC.plasmalogen", "C18.1.LPC", "bilirubin", "urobilin", "C16.0.SM" ], "rows": 65, "table": true, "tojson": true }, { "name": "FranzosaE_2019_Validation_CuratedMetadata", "title": "Franzosa et al. 2019 validation metadata", "object": "FranzosaE_2019_Validation_CuratedMetadata", "file": "FranzosaE_2019_Validation_CuratedMetadata.RData", "class": [ "data.frame" ], "fields": [ "X", "study_name", "Age", "BMI", "seq_type", "country", "Gender", "age_category", "body_site", "diseaseCat", "cohort_life_style", "MetabolomicsType", "Metabolomics_body_site", "Subject_ID", "diseaseCat_clean", "longitudinal", "sample_id" ], "rows": 65, "table": true, "tojson": true }, { "name": "FranzosaE_2019_Validation_CuratedSpeciesProfile", "title": "Franzosa et al. 2019 validation species profile", "object": "FranzosaE_2019_Validation_CuratedSpeciesProfile", "file": "FranzosaE_2019_Validation_CuratedSpeciesProfile.RData", "class": [ "data.frame" ], "fields": [ "X", "Abiotrophia_sp_HMSC24B09", "Absiella_dolichum", "Acetobacter_sp_CAG_267", "Acidaminococcus_intestini", "Actinobaculum_massiliense", "Actinobaculum_sp_oral_taxon_183", "Actinomyces_graevenitzii", "Actinomyces_johnsonii", "Actinomyces_massiliensis", "Actinomyces_naeslundii", "Actinomyces_odontolyticus", "Actinomyces_oris", "Actinomyces_radicidentis", "Actinomyces_sp_HMSC035G02", "Actinomyces_sp_HPA0247", "Actinomyces_sp_ICM47", "Actinomyces_sp_oral_taxon_181", "Actinomyces_sp_oral_taxon_448", "Actinomyces_turicensis", "Actinomyces_viscosus", "Agathobaculum_butyriciproducens", "Akkermansia_muciniphila", "Alistipes_finegoldii", "Alistipes_indistinctus", "Alistipes_inops", "Alistipes_obesi", "Alistipes_onderdonkii", "Alistipes_putredinis", "Alistipes_shahii", "Alistipes_sp_58_9_plus", "Alistipes_sp_An31A", "Alistipes_sp_CAG_268", "Alistipes_sp_CHKCI003", "Alistipes_timonensis", "Allisonella_histaminiformans", "Alloscardovia_omnicolens", "Anaerococcus_lactolyticus", "Anaerococcus_vaginalis", "Anaerofilum_sp_An201", "Anaeromassilibacillus_sp_An250", "Anaerostipes_caccae", "Anaerostipes_hadrus", "Anaerotignum_lactatifermentans", "Anaerotruncus_colihominis", "Asaccharobacter_celatus", "Atopobium_deltae", "Atopobium_minutum", "Atopobium_parvulum", "Atopobium_vaginae", "Azospirillum_sp_47_25", "Azospirillum_sp_CAG_260", "Bacteroides_caccae", "Bacteroides_cellulosilyticus", "Bacteroides_clarus", "Bacteroides_coagulans", "Bacteroides_coprocola", "Bacteroides_coprophilus", "Bacteroides_dorei", "Bacteroides_eggerthii", "Bacteroides_faecis", "Bacteroides_finegoldii", "Bacteroides_fluxus", "Bacteroides_fragilis", "Bacteroides_galacturonicus", "Bacteroides_intestinalis", "Bacteroides_massiliensis", "Bacteroides_nordii", "Bacteroides_ovatus", "Bacteroides_pectinophilus", "Bacteroides_plebeius", "Bacteroides_salyersiae", "Bacteroides_sp_CAG_1060", "Bacteroides_sp_CAG_1076", "Bacteroides_sp_CAG_144", "Bacteroides_sp_CAG_443", "Bacteroides_sp_CAG_530", "Bacteroides_sp_CAG_545", "Bacteroides_sp_CAG_709", "Bacteroides_sp_CAG_754", "Bacteroides_sp_CAG_875", "Bacteroides_sp_CAG_927", "Bacteroides_sp_D2", "Bacteroides_sp_OM08_11", "Bacteroides_stercorirosoris", "Bacteroides_stercoris", "Bacteroides_thetaiotaomicron", "Bacteroides_uniformis", "Bacteroides_vulgatus", "Bacteroides_xylanisolvens", "Barnesiella_intestinihominis", "Barnesiella_sp_An22", "Barnesiella_viscericola", "Bifidobacterium_adolescentis", "Bifidobacterium_animalis", "Bifidobacterium_bifidum", "Bifidobacterium_breve", "Bifidobacterium_catenulatum", "Bifidobacterium_dentium", "Bifidobacterium_gallinarum", "Bifidobacterium_kashiwanohense", "Bifidobacterium_longum", "Bifidobacterium_pseudocatenulatum", "Bifidobacterium_pullorum", "Bifidobacterium_saeculare", "Bifidobacterium_scardovii", "Bilophila_wadsworthia", "Blautia_coccoides", "Blautia_hansenii", "Blautia_hydrogenotrophica", "Blautia_obeum", "Blautia_producta", "Blautia_sp", "Blautia_sp_AF19_10LB", "Blautia_sp_An249", "Blautia_sp_CAG_257", "Blautia_sp_CAG_52", "Blautia_sp_N6H1_15", "Blautia_wexlerae", "Brochothrix_thermosphacta", "Butyricicoccus_porcorum", "Butyricicoccus_pullicaecorum", "Butyricimonas_sp", "Butyricimonas_synergistica", "Butyricimonas_virosa", "Butyrivibrio_crossotus", "Butyrivibrio_sp_CAG_318", "Campylobacter_hominis", "Campylobacter_showae", "Campylobacter_ureolyticus", "Candidatus_Gastranaerophilales_bacterium", "Candidatus_Gastranaerophilales_bacterium_HUM_10", "Candidatus_Gastranaerophilales_bacterium_HUM_11", "Candidatus_Gastranaerophilales_bacterium_HUM_18", "Candidatus_Gastranaerophilales_bacterium_HUM_21", "Candidatus_Melainabacteria_bacterium_35_41", "Carnobacterium_divergens", "Catabacter_hongkongensis", "Catenibacterium_mitsuokai", "Christensenella_minuta", "Citrobacter_amalonaticus", "Clostridiales_Family_XIII_bacterium", "Clostridiales_bacterium_1_7_47FAA", "Clostridiales_bacterium_CHKCI006", "Clostridiales_bacterium_KA00274", "Clostridiales_bacterium_KLE1615", "Clostridiales_bacterium_S5_A14a", "Clostridioides_difficile", "Clostridium_aldenense", "Clostridium_asparagiforme", "Clostridium_bolteae", "Clostridium_butyricum", "Clostridium_celatum", "Clostridium_citroniae", "Clostridium_clostridioforme", "Clostridium_disporicum", "Clostridium_hylemonae", "Clostridium_innocuum", "Clostridium_lavalense", "Clostridium_leptum", "Clostridium_methylpentosum", "Clostridium_paraputrificum", "Clostridium_perfringens", "Clostridium_saccharolyticum", "Clostridium_scindens", "Clostridium_sp_AF36_4", "Clostridium_sp_AM22_11AC", "Clostridium_sp_CAG_1193", "Clostridium_sp_CAG_122", "Clostridium_sp_CAG_12237_41", "Clostridium_sp_CAG_138", "Clostridium_sp_CAG_167", "Clostridium_sp_CAG_169", "Clostridium_sp_CAG_217", "Clostridium_sp_CAG_221", "Clostridium_sp_CAG_226", "Clostridium_sp_CAG_230", "Clostridium_sp_CAG_242", "Clostridium_sp_CAG_245", "Clostridium_sp_CAG_253", "Clostridium_sp_CAG_265", "Clostridium_sp_CAG_269", "Clostridium_sp_CAG_273", "Clostridium_sp_CAG_277", "Clostridium_sp_CAG_288", "Clostridium_sp_CAG_299", "Clostridium_sp_CAG_302", "Clostridium_sp_CAG_306", "Clostridium_sp_CAG_349", "Clostridium_sp_CAG_354", "Clostridium_sp_CAG_356", "Clostridium_sp_CAG_389", "Clostridium_sp_CAG_413", "Clostridium_sp_CAG_417", "Clostridium_sp_CAG_440", "Clostridium_sp_CAG_448", "Clostridium_sp_CAG_451", "Clostridium_sp_CAG_452", "Clostridium_sp_CAG_465", "Clostridium_sp_CAG_470", "Clostridium_sp_CAG_492", "Clostridium_sp_CAG_505", "Clostridium_sp_CAG_508", "Clostridium_sp_CAG_557", "Clostridium_sp_CAG_567", "Clostridium_sp_CAG_571", "Clostridium_sp_CAG_58", "Clostridium_sp_CAG_590", "Clostridium_sp_CAG_594", "Clostridium_sp_CAG_628", "Clostridium_sp_CAG_710", "Clostridium_sp_CAG_75", "Clostridium_sp_CAG_762", "Clostridium_sp_CAG_780", "Clostridium_sp_CAG_793", "Clostridium_sp_CAG_798", "Clostridium_sp_CAG_914", "Clostridium_sp_CAG_921", "Clostridium_sp_MSTE9", "Clostridium_spiroforme", "Clostridium_symbiosum", "Clostridium_ventriculi", "Collinsella_aerofaciens", "Collinsella_intestinalis", "Collinsella_massiliensis", "Collinsella_sp", "Collinsella_sp_An7", "Collinsella_sp_CAG_289", "Collinsella_stercoris", "Collinsella_tanakaei", "Coprobacillus_cateniformis", "Coprobacillus_sp_CAG_698", "Coprobacter_fastidiosus", "Coprobacter_secundus", "Coprococcus_catus", "Coprococcus_comes", "Coprococcus_eutactus", "Coraliomargarita_sp_CAG_312", "Corynebacterium_amycolatum", "Corynebacterium_durum", "Cryptobacterium_sp_CAG_338", "Desulfovibrio_desulfuricans", "Desulfovibrio_fairfieldensis", "Desulfovibrio_piger", "Desulfovibrionaceae_bacterium", "Dialister_invisus", "Dialister_micraerophilus", "Dialister_pneumosintes", "Dialister_sp_CAG_357", "Dialister_sp_CAG_486", "Dialister_succinatiphilus", "Dielma_fastidiosa", "Dorea_formicigenerans", "Dorea_longicatena", "Dorea_sp_CAG_317", "Dorea_sp_OM02_2LB", "Eggerthella_lenta", "Eggerthella_sinensis", "Eggerthella_sp_CAG_1427", "Eggerthella_sp_CAG_209", "Eggerthella_sp_CAG_298", "Eggerthella_sp_CAG_368", "Eisenbergiella_massiliensis", "Eisenbergiella_tayi", "Enorma_massiliensis", "Enterococcus_avium", "Enterococcus_casseliflavus", "Enterococcus_faecalis", "Enterococcus_faecium", "Enterococcus_gallinarum", "Enterococcus_phoeniculicola", "Enteroscipio_rubneri", "Erysipelatoclostridium_ramosum", "Erysipelotrichaceae_bacterium_3_1_53", "Escherichia_coli", "Eubacteriaceae_bacterium_CHKCI005", "Eubacterium_brachy", "Eubacterium_callanderi", "Eubacterium_eligens", "Eubacterium_hallii", "Eubacterium_limosum", "Eubacterium_pyruvativorans", "Eubacterium_ramulus", "Eubacterium_rectale", "Eubacterium_siraeum", "Eubacterium_sp_36_13", "Eubacterium_sp_AF17_7", "Eubacterium_sp_AM18_10LB_B", "Eubacterium_sp_An11", "Eubacterium_sp_CAG_115", "Eubacterium_sp_CAG_161", "Eubacterium_sp_CAG_180", "Eubacterium_sp_CAG_192", "Eubacterium_sp_CAG_251", "Eubacterium_sp_CAG_252", "Eubacterium_sp_CAG_274", "Eubacterium_sp_CAG_38", "Eubacterium_sp_CAG_581", "Eubacterium_sp_OM08_24", "Eubacterium_sp_TM05_53", "Eubacterium_sulci", "Eubacterium_ventriosum", "Faecalibacterium_prausnitzii", "Faecalibacterium_sp_CAG_74", "Faecalibacterium_sp_CAG_74_58_120", "Faecalicoccus_pleomorphus", "Faecalitalea_cylindroides", "Finegoldia_magna", "Firmicutes_bacterium_AF16_15", "Firmicutes_bacterium_AM10_47", "Firmicutes_bacterium_CAG_102", "Firmicutes_bacterium_CAG_103", "Firmicutes_bacterium_CAG_110", "Firmicutes_bacterium_CAG_114", "Firmicutes_bacterium_CAG_124", "Firmicutes_bacterium_CAG_129", "Firmicutes_bacterium_CAG_137", "Firmicutes_bacterium_CAG_145", "Firmicutes_bacterium_CAG_170", "Firmicutes_bacterium_CAG_176", "Firmicutes_bacterium_CAG_194", "Firmicutes_bacterium_CAG_238", "Firmicutes_bacterium_CAG_240", "Firmicutes_bacterium_CAG_24053_14", "Firmicutes_bacterium_CAG_272", "Firmicutes_bacterium_CAG_313", "Firmicutes_bacterium_CAG_321", "Firmicutes_bacterium_CAG_345", "Firmicutes_bacterium_CAG_41", "Firmicutes_bacterium_CAG_424", "Firmicutes_bacterium_CAG_460", "Firmicutes_bacterium_CAG_466", "Firmicutes_bacterium_CAG_475", "Firmicutes_bacterium_CAG_534", "Firmicutes_bacterium_CAG_555", "Firmicutes_bacterium_CAG_56", "Firmicutes_bacterium_CAG_582", "Firmicutes_bacterium_CAG_631", "Firmicutes_bacterium_CAG_646", "Firmicutes_bacterium_CAG_65_45_313", "Firmicutes_bacterium_CAG_83", "Firmicutes_bacterium_CAG_94", "Firmicutes_bacterium_CAG_95", "Flavonifractor_plautii", "Flavonifractor_sp_An10", "Flavonifractor_sp_An100", "Fusicatenibacter_saccharivorans", "Fusobacterium_gonidiaformans", "Fusobacterium_nucleatum", "Fusobacterium_sp_CAG_439", "Fusobacterium_ulcerans", "Gemella_morbillorum", "Gemella_sanguinis", "Gemmiger_formicilis", "Gemmiger_sp_An87", "Gordonibacter_pamelaeae", "Gordonibacter_sp_An232A", "Gordonibacter_urolithinfaciens", "Granulicatella_adiacens", "Haemophilus_parainfluenzae", "Hafnia_paralvei", "Holdemanella_biformis", "Holdemania_filiformis", "Hungatella_hathewayi", "Intestinibacter_bartlettii", "Intestinimonas_butyriciproducens", "Klebsiella_pneumoniae", "Klebsiella_quasipneumoniae", "Klebsiella_variicola", "Kosakonia_pseudosacchari", "Lachnoclostridium_sp_An118", "Lachnoclostridium_sp_An131", "Lachnoclostridium_sp_An138", "Lachnoclostridium_sp_An14", "Lachnoclostridium_sp_An181", "Lachnoclostridium_sp_An196", "Lachnospira_pectinoschiza", "Lachnospiraceae_bacterium_OF09_33XD", "Lachnospiraceae_bacterium_OF09_6", "Lachnospiraceae_bacterium_oral_taxon_096", "Lactobacillus_acidophilus", "Lactobacillus_algidus", "Lactobacillus_amylovorus", "Lactobacillus_antri", "Lactobacillus_casei_group", "Lactobacillus_curvatus", "Lactobacillus_delbrueckii", "Lactobacillus_fermentum", "Lactobacillus_gasseri", "Lactobacillus_iners", "Lactobacillus_kalixensis", "Lactobacillus_kullabergensis", "Lactobacillus_mucosae", "Lactobacillus_oris", "Lactobacillus_paragasseri", "Lactobacillus_plantarum", "Lactobacillus_reuteri", "Lactobacillus_rhamnosus", "Lactobacillus_ruminis", "Lactobacillus_saerimneri", "Lactobacillus_sakei", "Lactobacillus_salivarius", "Lactobacillus_vaccinostercus", "Lactococcus_lactis", "Lactonifactor_longoviformis", "Lawsonella_clevelandensis", "Lawsonibacter_asaccharolyticus", "Leuconostoc_carnosum", "Leuconostoc_garlicum", "Leuconostoc_gelidum", "Leuconostoc_mesenteroides", "Leuconostoc_pseudomesenteroides", "Massiliomicrobiota_timonensis", "Mediterraneibacter_sp_KCTC_15684", "Megamonas_funiformis", "Megasphaera_elsdenii", "Megasphaera_micronuciformis", "Megasphaera_sp_DISK_18", "Megasphaera_sp_MJR8396C", "Mesosutterella_multiformis", "Methanobrevibacter_smithii", "Methanosphaera_stadtmanae", "Mogibacterium_diversum", "Mogibacterium_timidum", "Monoglobus_pectinilyticus", "Murimonas_intestini", "Mycoplasma_sp_CAG_472", "Neisseria_flavescens", "Neisseria_subflava", "Odoribacter_laneus", "Odoribacter_splanchnicus", "Olsenella_profusa", "Olsenella_uli", "Oribacterium_sinus", "Oscillibacter_sp_57_20", "Oscillibacter_sp_CAG_155", "Oscillibacter_sp_CAG_241", "Oxalobacter_formigenes", "Parabacteroides_distasonis", "Parabacteroides_goldsteinii", "Parabacteroides_gordonii", "Parabacteroides_johnsonii", "Parabacteroides_merdae", "Parabacteroides_sp_CAG_409", "Paraeggerthella_hongkongensis", "Paraprevotella_clara", "Paraprevotella_xylaniphila", "Parascardovia_denticolens", "Parasutterella_excrementihominis", "Parvimonas_micra", "Parvimonas_sp_KA00067", "Pediococcus_acidilactici", "Pediococcus_pentosaceus", "Peptococcus_niger", "Peptoniphilus_coxii", "Peptoniphilus_duerdenii", "Peptoniphilus_harei", "Peptoniphilus_lacrimalis", "Peptoniphilus_sp_HMSC062D09", "Peptostreptococcaceae_bacterium_oral_taxon_929", "Peptostreptococcus_anaerobius", "Peptostreptococcus_sp_MV1", "Peptostreptococcus_stomatis", "Phascolarctobacterium_faecium", "Phascolarctobacterium_sp_CAG_266", "Phascolarctobacterium_succinatutens", "Porphyromonas_asaccharolytica", "Porphyromonas_sp_31_2", "Porphyromonas_sp_HMSC065F10", "Porphyromonas_uenonis", "Prevotella_bivia", "Prevotella_buccalis", "Prevotella_copri", "Prevotella_corporis", "Prevotella_disiens", "Prevotella_sp_109", "Prevotella_sp_CAG_1185", "Prevotella_sp_CAG_279", "Prevotella_sp_CAG_386", "Prevotella_sp_CAG_485", "Prevotella_sp_CAG_873", "Prevotella_timonensis", "Propionibacterium_acidifaciens", "Propionibacterium_freudenreichii", "Proteobacteria_bacterium_CAG_139", "Proteobacteria_bacterium_CAG_495", "Proteus_mirabilis", "Pseudoflavonifractor_capillosus", "Pseudoflavonifractor_sp_An184", "Pseudoramibacter_alactolyticus", "Romboutsia_ilealis", "Roseburia_faecis", "Roseburia_hominis", "Roseburia_intestinalis", "Roseburia_inulinivorans", "Roseburia_sp_CAG_100", "Roseburia_sp_CAG_10041_57", "Roseburia_sp_CAG_182", "Roseburia_sp_CAG_197", "Roseburia_sp_CAG_303", "Roseburia_sp_CAG_309", "Roseburia_sp_CAG_380", "Roseburia_sp_CAG_471", "Rothia_dentocariosa", "Rothia_mucilaginosa", "Rubneribacter_badeniensis", "Ruminococcaceae_bacterium_D16", "Ruminococcaceae_bacterium_D5", "Ruminococcaceae_bacterium_KLE1738", "Ruminococcus_bicirculans", "Ruminococcus_bromii", "Ruminococcus_callidus", "Ruminococcus_champanellensis", "Ruminococcus_gnavus", "Ruminococcus_lactaris", "Ruminococcus_sp_37_24", "Ruminococcus_sp_AF31_8BH", "Ruminococcus_sp_CAG_177", "Ruminococcus_sp_CAG_254", "Ruminococcus_sp_CAG_330", "Ruminococcus_sp_CAG_353", "Ruminococcus_sp_CAG_382", "Ruminococcus_sp_CAG_403", "Ruminococcus_sp_CAG_488", "Ruminococcus_sp_CAG_563", "Ruminococcus_sp_CAG_579", "Ruminococcus_torques", "Ruthenibacterium_lactatiformans", "Scardovia_wiggsiae", "Sellimonas_intestinalis", "Senegalimassilia_anaerobia", "Sharpea_azabuensis", "Slackia_isoflavoniconvertens", "Slackia_piriformis", "Solobacterium_moorei", "Staphylococcus_aureus", "Streptococcus_agalactiae", "Streptococcus_anginosus_group", "Streptococcus_australis", "Streptococcus_downei", "Streptococcus_gallolyticus", "Streptococcus_gordonii", "Streptococcus_infantis", "Streptococcus_milleri", "Streptococcus_mitis", "Streptococcus_mutans", "Streptococcus_oralis", "Streptococcus_parasanguinis", "Streptococcus_pasteurianus", "Streptococcus_pseudopneumoniae", "Streptococcus_salivarius", "Streptococcus_sanguinis", "Streptococcus_sobrinus", "Streptococcus_sp_A12", "Streptococcus_sp_F0442", "Streptococcus_thermophilus", "Streptococcus_vestibularis", "Subdoligranulum_sp", "Subdoligranulum_sp_APC924_74", "Sutterella_sp_CAG_351", "Sutterella_sp_CAG_521", "Sutterella_wadsworthensis", "Terrisporobacter_othiniensis", "Turicibacter_sanguinis", "Tyzzerella_nexilis", "Tyzzerella_sp", "Varibaculum_cambriense", "Veillonella_atypica", "Veillonella_dispar", "Veillonella_infantium", "Veillonella_parvula", "Veillonella_seminalis", "Veillonella_sp_CAG_933", "Veillonella_sp_DORA_A_3_16_22", "Veillonella_sp_T11011_6", "Victivallales_bacterium_CCUG_44730", "Weissella_viridescens" ], "rows": 65, "table": true, "tojson": true }, { "name": "gene_all", "title": "TCGA BRCA gene-level table", "object": "gene_all", "file": "gene_all.RData", "class": [ "data.frame" ], "fields": [ "patient_id", "OS", "OS.time", "age", "race_white", "stage_i", "stage_ii", "ENSG00000000938", "ENSG00000000971", "ENSG00000001461", "ENSG00000001630", "ENSG00000003989", "ENSG00000004139", "ENSG00000004455", "ENSG00000004487", "ENSG00000004777", "ENSG00000004779", "ENSG00000005108", "ENSG00000005206", "ENSG00000005243", "ENSG00000005249", "ENSG00000005302", "ENSG00000005812", "ENSG00000005882", "ENSG00000005884", "ENSG00000006071", "ENSG00000006210", "ENSG00000006327", "ENSG00000006634", "ENSG00000007312", "ENSG00000007402", "ENSG00000008394", "ENSG00000008441", "ENSG00000008513", "ENSG00000008516", "ENSG00000008517", "ENSG00000008988", "ENSG00000010310", "ENSG00000010361", "ENSG00000011007", "ENSG00000011021", "ENSG00000011201", "ENSG00000011677", "ENSG00000012048", "ENSG00000012223", "ENSG00000012232", "ENSG00000013619", "ENSG00000014138", "ENSG00000015285", "ENSG00000015413", "ENSG00000017427", "ENSG00000017483", "ENSG00000019582", "ENSG00000023445", "ENSG00000025039", "ENSG00000027075", "ENSG00000027697", "ENSG00000031081", "ENSG00000032219", "ENSG00000032742", "ENSG00000033327", "ENSG00000035499", "ENSG00000035862", "ENSG00000038295", "ENSG00000038945", "ENSG00000039123", "ENSG00000043143", "ENSG00000043462", "ENSG00000043591", "ENSG00000044446", "ENSG00000047410", "ENSG00000047457", "ENSG00000048462", "ENSG00000049323", "ENSG00000049540", "ENSG00000051523", "ENSG00000053371", "ENSG00000053747", "ENSG00000054282", "ENSG00000054392", "ENSG00000055118", "ENSG00000055732", "ENSG00000056998", "ENSG00000057593", "ENSG00000058063", "ENSG00000058085", "ENSG00000058272", "ENSG00000058335", "ENSG00000059377", "ENSG00000060642", "ENSG00000060718", "ENSG00000061273", "ENSG00000062038", "ENSG00000063176", "ENSG00000063854", "ENSG00000064270", "ENSG00000064309", "ENSG00000064655", "ENSG00000064989", "ENSG00000065320", "ENSG00000065559", "ENSG00000066735", "ENSG00000066933", "ENSG00000067141", "ENSG00000068024", "ENSG00000068078", "ENSG00000068366", "ENSG00000068650", "ENSG00000068796", "ENSG00000069248", "ENSG00000069424", "ENSG00000069696", "ENSG00000069869", "ENSG00000070010", "ENSG00000070190", "ENSG00000070193", "ENSG00000070366", "ENSG00000070770", "ENSG00000071073", "ENSG00000071242", "ENSG00000071282", "ENSG00000071553", "ENSG00000071967", "ENSG00000072210", "ENSG00000072310", "ENSG00000072694", "ENSG00000072952", "ENSG00000073282", "ENSG00000073464", "ENSG00000073756", "ENSG00000073849", "ENSG00000074047", "ENSG00000074219", "ENSG00000074319", "ENSG00000074370", "ENSG00000074416", "ENSG00000074527", "ENSG00000075218", "ENSG00000075239", "ENSG00000075340", "ENSG00000075914", "ENSG00000075945", "ENSG00000076003", "ENSG00000076555", "ENSG00000076662", "ENSG00000076864", "ENSG00000076984", "ENSG00000077044", "ENSG00000077092", "ENSG00000077150", "ENSG00000077274", "ENSG00000078070", "ENSG00000078269", "ENSG00000078295", "ENSG00000078401", "ENSG00000078589", "ENSG00000078674", "ENSG00000078902", "ENSG00000079335", "ENSG00000079435", "ENSG00000080503", "ENSG00000080986", "ENSG00000081041", "ENSG00000081052", "ENSG00000081237", "ENSG00000081377", "ENSG00000082014", "ENSG00000082074", "ENSG00000082175", "ENSG00000082701", "ENSG00000082898", "ENSG00000083642", "ENSG00000084207", "ENSG00000084636", "ENSG00000084731", "ENSG00000085563", "ENSG00000085741", "ENSG00000085788", "ENSG00000085978", "ENSG00000086548", "ENSG00000086619", "ENSG00000086730", "ENSG00000087086", "ENSG00000087245", "ENSG00000087253", "ENSG00000087494", "ENSG00000087510", "ENSG00000087586", "ENSG00000088256", "ENSG00000088387", "ENSG00000088827", "ENSG00000088888", "ENSG00000089012", "ENSG00000089127", "ENSG00000089159", "ENSG00000089195", "ENSG00000089280", "ENSG00000089472", "ENSG00000090104", "ENSG00000090382", "ENSG00000090554", "ENSG00000090659", "ENSG00000090861", "ENSG00000090889", "ENSG00000091073", "ENSG00000091127", "ENSG00000091428", "ENSG00000091483", "ENSG00000091879", "ENSG00000091972", "ENSG00000092421", "ENSG00000092758", "ENSG00000093009", "ENSG00000093072", "ENSG00000094804", "ENSG00000095015", "ENSG00000095319", "ENSG00000095585", "ENSG00000095627", "ENSG00000095739", "ENSG00000096433", "ENSG00000096968", "ENSG00000097007", "ENSG00000097021", "ENSG00000097046", "ENSG00000099250", "ENSG00000099769" ], "rows": 320, "table": true, "tojson": true }, { "name": "mir_all", "title": "TCGA BRCA microRNA-level table", "object": "mir_all", "file": "mir_all.RData", "class": [ "data.frame" ], "fields": [ "patient_id", "OS", "OS.time", "age", "race_white", "stage_i", "stage_ii", "hsa.let.7d", "hsa.let.7f.1", "hsa.let.7f.2", "hsa.let.7g", "hsa.mir.100", "hsa.mir.101.1", "hsa.mir.101.2", "hsa.mir.103a.1", "hsa.mir.103a.2", "hsa.mir.105.1", "hsa.mir.105.2", "hsa.mir.106a", "hsa.mir.106b", "hsa.mir.10a", "hsa.mir.10b", "hsa.mir.1180", "hsa.mir.1181", "hsa.mir.1185.2", "hsa.mir.1224", "hsa.mir.1226", "hsa.mir.1227", "hsa.mir.1228", "hsa.mir.1229", "hsa.mir.1236", "hsa.mir.1237", "hsa.mir.1243", "hsa.mir.1245a", "hsa.mir.1247", "hsa.mir.1249", "hsa.mir.1250", "hsa.mir.1251", "hsa.mir.1254.1", "hsa.mir.1254.2", "hsa.mir.1258", "hsa.mir.126", "hsa.mir.1262", "hsa.mir.1269a", "hsa.mir.1269b", "hsa.mir.1270", "hsa.mir.1271", "hsa.mir.1277", "hsa.mir.1278", "hsa.mir.1284", "hsa.mir.1288", "hsa.mir.1291", "hsa.mir.1292", "hsa.mir.1294", "hsa.mir.1295a", "hsa.mir.1301", "hsa.mir.1304", "hsa.mir.1306", "hsa.mir.1307", "hsa.mir.130a", "hsa.mir.1343", "hsa.mir.135b", "hsa.mir.139", "hsa.mir.142", "hsa.mir.145", "hsa.mir.1468", "hsa.mir.146a", "hsa.mir.146b", "hsa.mir.147b", "hsa.mir.148b", "hsa.mir.149", "hsa.mir.150", "hsa.mir.151b", "hsa.mir.152", "hsa.mir.153.1", "hsa.mir.153.2", "hsa.mir.1537", "hsa.mir.154", "hsa.mir.155", "hsa.mir.15a", "hsa.mir.16.1", "hsa.mir.16.2", "hsa.mir.17", "hsa.mir.182", "hsa.mir.183", "hsa.mir.184", "hsa.mir.185", "hsa.mir.187", "hsa.mir.188", "hsa.mir.18a", "hsa.mir.18b", "hsa.mir.190b", "hsa.mir.191", "hsa.mir.1910", "hsa.mir.1914", "hsa.mir.193b", "hsa.mir.195", "hsa.mir.196a.1", "hsa.mir.196a.2", "hsa.mir.197", "hsa.mir.19a", "hsa.mir.202", "hsa.mir.203b", "hsa.mir.204", "hsa.mir.205", "hsa.mir.20a", "hsa.mir.20b", "hsa.mir.21", "hsa.mir.210", "hsa.mir.2110", "hsa.mir.2114", "hsa.mir.2115", "hsa.mir.2116", "hsa.mir.215", "hsa.mir.218.2", "hsa.mir.219a.1", "hsa.mir.224", "hsa.mir.2276", "hsa.mir.2277", "hsa.mir.2355", "hsa.mir.23b", "hsa.mir.24.1", "hsa.mir.24.2", "hsa.mir.26a.2", "hsa.mir.27a", "hsa.mir.27b", "hsa.mir.296", "hsa.mir.299", "hsa.mir.29b.1", "hsa.mir.29b.2", "hsa.mir.29c", "hsa.mir.301a", "hsa.mir.301b", "hsa.mir.3064", "hsa.mir.3065", "hsa.mir.3074", "hsa.mir.30a", "hsa.mir.30b", "hsa.mir.30c.1", "hsa.mir.30c.2", "hsa.mir.31", "hsa.mir.3117", "hsa.mir.3124", "hsa.mir.3126", "hsa.mir.3127", "hsa.mir.3129", "hsa.mir.3130.1" ], "rows": 320, "table": true, "tojson": true }, { "name": "NLIBD", "title": "NLIBD binary-outcome PCL fixture", "object": "NLIBD", "file": "NLIBD.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "pregnancy", "title": "Pregnancy continuous-outcome PCL fixture", "object": "pregnancy", "file": "pregnancy.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "PRISM", "title": "PRISM binary-outcome PCL fixture", "object": "PRISM", "file": "PRISM.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "auc.obj", "title": "Title Meta level Objective function: NNLS for gaussian; Rank loss for binary observations", "topics": [ "auc.obj" ] }, { "page": "FranzosaE_2019_CuratedMetabolome", "title": "Franzosa et al. 2019 training metabolome table", "topics": [ "FranzosaE_2019_CuratedMetabolome" ] }, { "page": "FranzosaE_2019_CuratedMetadata", "title": "Franzosa et al. 2019 training metadata", "topics": [ "FranzosaE_2019_CuratedMetadata" ] }, { "page": "FranzosaE_2019_CuratedSpeciesProfile", "title": "Franzosa et al. 2019 training species profile", "topics": [ "FranzosaE_2019_CuratedSpeciesProfile" ] }, { "page": "FranzosaE_2019_Validation_CuratedMetabolome", "title": "Franzosa et al. 2019 validation metabolome table", "topics": [ "FranzosaE_2019_Validation_CuratedMetabolome" ] }, { "page": "FranzosaE_2019_Validation_CuratedMetadata", "title": "Franzosa et al. 2019 validation metadata", "topics": [ "FranzosaE_2019_Validation_CuratedMetadata" ] }, { "page": "FranzosaE_2019_Validation_CuratedSpeciesProfile", "title": "Franzosa et al. 2019 validation species profile", "topics": [ "FranzosaE_2019_Validation_CuratedSpeciesProfile" ] }, { "page": "gene_all", "title": "TCGA BRCA gene-level table", "topics": [ "gene_all" ] }, { "page": "IL_conbin", "title": "Integrated machine learning for multi-omics prediction (continuous/binary outcomes)", "topics": [ "IL_conbin" ] }, { "page": "IL_multiclass", "title": "Integrated machine learning for multi-omics multiclass classification", "topics": [ "IL_multiclass" ] }, { "page": "ILsurv", "title": "IntegratedLearner Survival Engine", "topics": [ "ILsurv", "IL_survival" ] }, { "page": "IntegratedLearner", "title": "Integrated machine learning for multi-omics prediction and classification", "topics": [ "IntegratedLearner" ] }, { "page": "mir_all", "title": "TCGA BRCA microRNA-level table", "topics": [ "mir_all" ] }, { "page": "NLIBD", "title": "NLIBD binary-outcome PCL fixture", "topics": [ "NLIBD" ] }, { "page": "NNLS", "title": "NNLS function to optimize weights of several base learners", "topics": [ "NNLS" ] }, { "page": "plot.learner", "title": "Plot the summary curves produced by an IntegratedLearner object", "topics": [ "plot.learner" ] }, { "page": "predict.learner", "title": "Make predictions using a trained 'IntegratedLearner' model", "topics": [ "predict.learner" ] }, { "page": "predict.SL.BART", "title": "Predict function for SL.BART", "topics": [ "predict.SL.BART" ] }, { "page": "predict.SL.nnls.auc", "title": "Predict function for SL.nnls.auc", "topics": [ "predict.SL.nnls.auc" ] }, { "page": "pregnancy", "title": "Pregnancy continuous-outcome PCL fixture", "topics": [ "pregnancy" ] }, { "page": "PRISM", "title": "PRISM binary-outcome PCL fixture", "topics": [ "PRISM" ] }, { "page": "SL.BART", "title": "Wrapper for bartMachine learner", "topics": [ "SL.BART" ] }, { "page": "SL.enet", "title": "Elastic net regression, including lasso and ridge with optimized alpha and lambda", "topics": [ "SL.enet" ] }, { "page": "SL.glmnet2", "title": "Elastic net regression, including lasso and ridge with a fixed alpha", "topics": [ "SL.glmnet2" ] }, { "page": "SL.horseshoe", "title": "Horseshoe regression", "topics": [ "SL.horseshoe" ] }, { "page": "SL.LASSO", "title": "Elastic net regression, including lasso and ridge with a fixed alpha", "topics": [ "SL.LASSO" ] }, { "page": "SL.mxBART", "title": "mxBART SuperLearner wrapper", "topics": [ "SL.mxBART" ] }, { "page": "SL.nnls.auc", "title": "Combined SuperLearner function for both NNLS/AUC maximization", "topics": [ "SL.nnls.auc" ] }, { "page": "update.learner", "title": "Update IntegratedLearner fit object based on layers available in the test set", "topics": [ "update.learner" ] } ], "_readme": "https://github.com/BiocStaging/IntegratedLearner/raw/HEAD/README.md", "_rundeps": [ "abind", "Biobase", "BiocBaseUtils", "BiocGenerics", "bitops", "caret", "caTools", "class", "cli", "clock", "codetools", "cpp11", "cvAUC", "data.table", "DelayedArray", "diagram", "digest", "dplyr", "e1071", "farver", "foreach", "future", "future.apply", "gam", "generics", "GenomicRanges", "ggplot2", "glmnet", "globals", "glue", "gower", "gplots", "gtable", "gtools", "hardhat", "ipred", "IRanges", "isoband", "iterators", "KernSmooth", "labeling", "lattice", "lava", "lifecycle", "listenv", "lubridate", "magrittr", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "ModelMetrics", "MultiAssayExperiment", "nlme", "nnet", "nnls", "numDeriv", "parallelly", "pillar", "pkgconfig", "plyr", "pROC", "prodlim", "progressr", "proxy", "purrr", "R6", "ranger", "RColorBrewer", "Rcpp", "RcppEigen", "recipes", "reshape2", "rlang", "ROCR", "rpart", "S4Arrays", "S4Vectors", "S7", "scales", "Seqinfo", "shape", "SparseArray", "sparsevctrs", "SQUAREM", "stringi", "stringr", "SummarizedExperiment", "SuperLearner", "survival", "tibble", "tidyr", "tidyselect", "timechange", "timeDate", "tzdb", "utf8", "vctrs", "viridisLite", "withr", "XVector" ], "_vignettes": [ { "source": "IntegratedLearner.Rmd", "filename": "IntegratedLearner.html", "title": "IntegratedLearner", "author": "Nalin Arora, Anupreet Porwal and Himel Mallick", "engine": "knitr::rmarkdown", "headings": [ "Load Packages", "Input Data Contract", "Alternative Input Mode: MAE (Complete Binary Example)", "Parameter Reference (Conbin, Multiclass, and Survival)", "Common Wrapper Parameters (IntegratedLearner)", "Conbin-Specific Parameters (Continuous/Binary Path)", "Multiclass-Specific Parameters (Native Multiclass Path)", "Survival-Specific Parameters (via ...)", "Supported Models and Fusion Modules", "Supported Models", "Supported Fusion Outputs", "Output Reference: What You Get and How to Access It", "Conbin Outputs (Binary/Continuous)", "Multiclass Outputs", "Survival Outputs (Single/Early/Late)", "Importance Outputs (Conbin, Multiclass, and Survival)", "Quick Access Snippets", "Example 1: Binary Outcome (IBD Classification)", "Step 1: Load and Inspect Training and Validation Data", "Step 2: Build PCL Inputs", "Step 3: Fit the Model", "Step 4: Inspect and Interpret Outputs", "Example 2: Continuous Outcome (Gestational Age)", "Step 1: Load and Inspect Data", "Step 2: Build PCL Input", "Step 3: Fit Continuous Model", "Step 4: Evaluate Predictive Accuracy", "Step 5: Uncertainty and Feature-Level Interpretation (BART)", "Example 3: Multiclass Outcome (Franzosa MAE with External Validation)", "Example 4: Survival Outcome (Time-to-event)", "Interpret Survival Outputs", "Session Information", "References", "Citation" ], "created": "2025-11-13 19:16:37", "modified": "2026-06-09 11:17:34", "commits": 17 } ], "_score": 4.1875207208364635, "_indexed": true, "_nocasepkg": "integratedlearner", "_universes": [ "biocstaging", "himelmallick" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.99.0", "date": "2026-06-09T13:51:40.000Z", "distro": "noble", "commit": "2952c7c8eef230756be15d59837d648871049044", "fileid": "df166afa21ad002529c1fa9213368d7b88a7528a8b0e15dfd2646109837098d9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/27210370344" }, { "r": "4.6.0", "os": "linux", "version": "0.99.0", "date": "2026-06-09T13:51:52.000Z", "distro": "noble", "commit": "2952c7c8eef230756be15d59837d648871049044", "fileid": "e4b630bcb3f0444d99c74c42f317e0b6e3f2a1cdf1f1362ef27b71661cca732c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/27210370344" }, { "r": "4.5.3", "os": "mac", "version": "0.99.0", "date": "2026-06-09T13:52:41.000Z", "commit": "2952c7c8eef230756be15d59837d648871049044", "fileid": "f4e432ee706a730a3054b8a488266743eea16591f03467af817db671887b57ee", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/27210370344" }, { "r": "4.6.0", "os": "mac", "version": "0.99.0", "date": "2026-06-09T13:52:30.000Z", "commit": "2952c7c8eef230756be15d59837d648871049044", "fileid": "1629347a5c8e4768c71aef77ef3e3cdf5638a90318560e5dd5d4da1e398d272f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/27210370344" }, { "r": "4.6.0", "os": "wasm", "version": "0.99.0", "date": "2026-06-09T13:51:44.000Z", "commit": "2952c7c8eef230756be15d59837d648871049044", "fileid": "757a73d3a46edf261d672e234569e7ab6b21518d5c55004be7fa3cdb29cb5d16", "status": "success", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/27210370344" }, { "r": "4.7.0", "os": "win", "version": "0.99.0", "date": "2026-06-09T13:50:17.000Z", "commit": "2952c7c8eef230756be15d59837d648871049044", "fileid": "81dbcb97c98ac18ed610083a38dc7758d749f91440883907085f20f2a55e14f6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/27210370344" }, { "r": "4.5.3", "os": "win", "version": "0.99.0", "date": "2026-06-09T13:50:29.000Z", "commit": "2952c7c8eef230756be15d59837d648871049044", "fileid": "dda0c7f4b643c285256b87bc32589d79beb884fb4fcd11178f6e70b9a2e11a83", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/27210370344" }, { "r": "4.6.0", "os": "win", "version": "0.99.0", "date": "2026-06-09T13:50:23.000Z", "commit": "2952c7c8eef230756be15d59837d648871049044", "fileid": "6092f4ad0b80d153539e3824c29e9bc67090818e98476510853599694dc9d800", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/27210370344" } ] }