{
  "_id": "6a1aeac31d7bb097a09f36d1",
  "Package": "SIAMCAT",
  "Type": "Package",
  "Title": "Statistical Inference of Associations between Microbial\nCommunities And host phenoTypes",
  "Version": "2.17.0",
  "Authors@R": "c(person(\"Konrad\", \"Zych\", role = c(\"aut\"),\nemail = \"konrad.zych@embl.de\",\ncomment = c(ORCID = \"0000-0001-7426-0516\")),\nperson(\"Jakob\", \"Wirbel\", role = c(\"aut\", \"cre\"),\nemail = \"jakob.wirbel@embl.de\",\ncomment = c(ORCID = \"0000-0002-4073-3562\")),\nperson(\"Georg\", \"Zeller\", role = c(\"aut\"),\nemail = \"zeller@embl.de\",\ncomment = c(ORCID = \"0000-0003-1429-7485\")),\nperson(\"Morgan\", \"Essex\",\nemail = \"morgan.essex@embl.de\", role = c(\"ctb\")),\nperson(\"Nicolai\", \"Karcher\", role = c(\"ctb\")),\nperson(\"Kersten\", \"Breuer\", role = c(\"ctb\")))",
  "Description": "Pipeline for Statistical Inference of Associations between\nMicrobial Communities And host phenoTypes (SIAMCAT). A primary\ngoal of analyzing microbiome data is to determine changes in\ncommunity composition that are associated with environmental\nfactors. In particular, linking human microbiome composition to\nhost phenotypes such as diseases has become an area of intense\nresearch. For this, robust statistical modeling and biomarker\nextraction toolkits are crucially needed. SIAMCAT provides a\nfull pipeline supporting data preprocessing, statistical\nassociation testing, statistical modeling (LASSO logistic\nregression) including tools for evaluation and interpretation\nof these models (such as cross validation, parameter selection,\nROC analysis and diagnostic model plots).",
  "License": "GPL-3",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:48:00 UTC",
  "RemoteUrl": "https://github.com/bioc/SIAMCAT",
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  "Author": "Konrad Zych [aut] (ORCID: <https://orcid.org/0000-0001-7426-0516>),\nJakob Wirbel [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-4073-3562>),\nGeorg Zeller [aut] (ORCID: <https://orcid.org/0000-0003-1429-7485>),\nMorgan Essex [ctb],\nNicolai Karcher [ctb],\nKersten Breuer [ctb]",
  "Maintainer": "Jakob Wirbel <jakob.wirbel@embl.de>",
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  "_published": "2026-05-30T13:48:50.946Z",
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    "classification",
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    "featureextraction",
    "geneticvariability",
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    "model_list<-",
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    "read.lefse",
    "select.samples",
    "siamcat",
    "siamcat.to.lefse",
    "siamcat.to.maaslin",
    "summarize.features",
    "train.model",
    "validate.data",
    "volcano.plot",
    "weight_matrix"
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      "title": "Example feature matrix",
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      "title": "Example metadata matrix",
      "object": "meta_crc_zeller",
      "class": [
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      "fields": [
        "Age",
        "BMI",
        "Gender",
        "AJCC_stage",
        "FOBT",
        "Group"
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    {
      "name": "siamcat_example",
      "title": "SIAMCAT example",
      "object": "siamcat_example",
      "class": [
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  "_help": [
    {
      "page": "SIAMCAT-package",
      "title": "SIAMCAT: Statistical Inference of Associations between Microbial Communities And host phenoTypes",
      "topics": [
        "SIAMCAT-package",
        "SIAMCAT"
      ]
    },
    {
      "page": "add.meta.pred",
      "title": "Add metadata as predictors",
      "topics": [
        "add.meta.pred"
      ]
    },
    {
      "page": "assoc_param-methods",
      "title": "Retrieve the list of parameters for association testing from a SIAMCAT object",
      "topics": [
        "assoc_param",
        "assoc_param,siamcat-method",
        "assoc_param_param"
      ]
    },
    {
      "page": "association.plot",
      "title": "Visualize associations between features and classes",
      "topics": [
        "association.plot"
      ]
    },
    {
      "page": "associations-methods",
      "title": "Retrieve the results of association testing from a SIAMCAT object",
      "topics": [
        "associations",
        "associations,siamcat-method"
      ]
    },
    {
      "page": "check.associations",
      "title": "Calculate associations between features and labels",
      "topics": [
        "check.associations"
      ]
    },
    {
      "page": "check.confounders",
      "title": "Check for potential confounders in the metadata",
      "topics": [
        "check.confounders"
      ]
    },
    {
      "page": "create.data.split",
      "title": "Split a dataset into training and a test sets.",
      "topics": [
        "create.data.split"
      ]
    },
    {
      "page": "create.label",
      "title": "Create a label list",
      "topics": [
        "create.label"
      ]
    },
    {
      "page": "data_split-methods",
      "title": "Retrieve the data split from a SIAMCAT object",
      "topics": [
        "data_split",
        "data_split,siamcat-method"
      ]
    },
    {
      "page": "eval_data-methods",
      "title": "Retrieve the evaluation metrics from a SIAMCAT object",
      "topics": [
        "eval_data",
        "eval_data,siamcat-method"
      ]
    },
    {
      "page": "evaluate.predictions",
      "title": "Evaluate prediction results",
      "topics": [
        "evaluate.predictions"
      ]
    },
    {
      "page": "feat.crc.zeller",
      "title": "Example feature matrix",
      "topics": [
        "feat.crc.zeller"
      ]
    },
    {
      "page": "feature_type-methods",
      "title": "Retrieve the feature type used for model training from a SIAMCAT object",
      "topics": [
        "feature_type",
        "feature_type,siamcat-method"
      ]
    },
    {
      "page": "feature_weights-methods",
      "title": "Retrieve the matrix of feature weights from a SIAMCAT object",
      "topics": [
        "feature_weights",
        "feature_weights,siamcat-method"
      ]
    },
    {
      "page": "filt_params-methods",
      "title": "Retrieve the list of parameters for feature filtering from a SIAMCAT object",
      "topics": [
        "filt_params",
        "filt_params,siamcat-method"
      ]
    },
    {
      "page": "filter.features",
      "title": "Perform unsupervised feature filtering.",
      "topics": [
        "filter.features"
      ]
    },
    {
      "page": "filter.label",
      "title": "Filter the label of a SIMACAT object",
      "topics": [
        "filter.label"
      ]
    },
    {
      "page": "get.filt_feat.matrix",
      "title": "Retrieve the filtered features from a SIAMCAT object",
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      "title": "Retrieve the normalized features from a SIAMCAT object",
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    {
      "page": "weight_matrix-methods",
      "title": "Retrieve the weight matrix from a SIAMCAT object",
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