{ "_id": "6a212632cd65a98ecbd20cdd", "Package": "PIUMA", "Type": "Package", "Title": "Phenotypes Identification Using Mapper from topological data\nAnalysis", "Version": "1.9.0", "Authors@R": "c(\nperson(\"Mattia\", \"Chiesa\", , \"mattia.chiesa@cardiologicomonzino.it\",\nrole = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0001-7427-9954\")),\nperson(\"Arianna\", \"Dagliati\", , \"arianna.dagliati@unipv.it\",\nrole = \"aut\", comment = c(ORCID = \"0000-0002-5041-0409\")),\nperson(\"Alessia\", \"Gerbasi\", , \"alessia.gerbasi01@universitadipavia.it\",\nrole = \"aut\", comment = c(ORCID = \"0000-0003-4501-1777\")),\nperson(\"Giuseppe\", \"Albi\", , \"giuseppe.albi01@universitadipavia.it\",\nrole = \"aut\"),\nperson(\"Laura\", \"Ballarini\", , \"laura.ballarini01@universitadipavia.it\",\nrole = \"aut\"),\nperson(\"Luca\", \"Piacentini\", , \"luca.piacentini@cardiologicomonzino.it\",\nrole = \"aut\", comment = c(ORCID = \"0000-0003-1022-4481\")),\nperson(\"Carlo\", \"Leonardi\", , \"cl35@sanger.ac.uk\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0001-5348-8300\"))\n)", "Description": "The PIUMA package offers a tidy pipeline of Topological\nData Analysis frameworks to identify and characterize\ncommunities in high and heterogeneous dimensional data.", "License": "GPL-3 + file LICENSE", "Encoding": "UTF-8", "LazyData": "false", "biocViews": "Clustering, GraphAndNetwork, DimensionReduction, Network,\nClassification", "VignetteBuilder": "knitr", "RoxygenNote": "7.3.1", "URL": "https://github.com/BioinfoMonzino/PIUMA", "BugReports": "https://github.com/BioinfoMonzino/PIUMA/issues", "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libpng-dev\nlibuv1-dev libxml2-dev libssl-dev python3 zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 13:02:54 UTC", "RemoteUrl": "https://github.com/bioc/PIUMA", "RemoteRef": "HEAD", "RemoteSha": "c00b5d79824d3bdeedb5bbc5c798c24715c61fc4", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-04 07:08:22 UTC", "User": "root" }, "Author": "Mattia Chiesa [aut, cre] (ORCID:\n),\nArianna Dagliati [aut] (ORCID: ),\nAlessia Gerbasi [aut] (ORCID: ),\nGiuseppe Albi [aut],\nLaura Ballarini [aut],\nLuca Piacentini [aut] (ORCID: ),\nCarlo Leonardi [aut] (ORCID: )", "Maintainer": "Mattia Chiesa ", "MD5sum": "3174ead9cd47d09241f1d277f1bdd6c2", "_user": "bioc", "_type": "src", "_file": "PIUMA_1.9.0.tar.gz", "_fileid": "0ff7bc6cb4342958e964bf2612349b851712fcba3205e0be02e2b0eea242ade1", "_filesize": 5070758, "_sha256": "0ff7bc6cb4342958e964bf2612349b851712fcba3205e0be02e2b0eea242ade1", "_created": "2026-06-04T07:08:22.000Z", "_published": "2026-06-04T07:16:02.536Z", "_jobs": [ { "job": 79467807416, "time": 184, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7405222133" }, { "job": 79467807517, "time": 394, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7405280682" }, { "job": 79467807438, "time": 383, "config": 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"page": "autoClusterMapper", "title": "Automatic Clustering of a Mapper Graph by Predicted Geometry (with kNN tie-break)", "topics": [ "autoClusterMapper" ] }, { "page": "checkNetEntropy", "title": "Compute the Network Entropy", "topics": [ "checkNetEntropy" ] }, { "page": "checkScaleFreeModel", "title": "Assessment of Scale-Free model fitting", "topics": [ "checkScaleFreeModel" ] }, { "page": "df_test_proj", "title": "A dataset to test the 'dfToProjection' and 'dfToDistance' funtions of 'PIUMA' package.", "topics": [ "df_test_proj" ] }, { "page": "dfToDistance", "title": "Compute the Distance Matrix from TDAobj", "topics": [ "dfToDistance" ] }, { "page": "dfToProjection", "title": "Data projection using a Dimensionality Reduction Method", "topics": [ "dfToProjection" ] }, { "page": "getClusters", "title": "Getter method for the 'clustering' slot of a TDAobj object.", "topics": [ "getClusters", "getClusters,PIUMA-getClusters", "getClusters,TDAobj-method" ] }, { "page": "getComp", "title": "Getter method for the 'comp' slot of a TDAobj object.", "topics": [ "getComp", "getComp,PIUMA-getComp", "getComp,TDAobj-method" ] }, { "page": "getDfMapper", "title": "Getter method for the 'dfMapper' slot of a TDAobj object.", "topics": [ "getDfMapper", "getDfMapper,PIUMA-getDfMapper", "getDfMapper,TDAobj-method" ] }, { "page": "getDistMat", "title": "Getter method for the 'dist_mat' slot of a TDAobj object.", "topics": [ "getDistMat", "getDistMat,PIUMA-getDistMat", "getDistMat,TDAobj-method" ] }, { "page": "getGraph", "title": "Getter method for the 'graph' slot of a TDAobj object.", "topics": [ "getGraph", "getGraph,PIUMA-getGraph", "getGraph,TDAobj-method" ] }, { "page": "getJacc", "title": "Getter method for the 'jacc' slot of a TDAobj object.", "topics": [ "getJacc", "getJacc,PIUMA-getJacc", "getJacc,TDAobj-method" ] }, { "page": "getMetrics", "title": "Getter method for the 'metrics' slot under 'graph' of a TDAobj object.", "topics": [ "getMetric,PIUMA-getMetrics", "getMetrics", "getMetrics,TDAobj-method" ] }, { "page": "getNodeDataMat", "title": "Getter method for the 'node_data_mat' slot of a TDAobj object.", "topics": [ "getNodeDataMat", "getNodeDataMat,PIUMA-getNodeDataMat", "getNodeDataMat,TDAobj-method" ] }, { "page": "getOrigData", "title": "Getter method for the 'orig_data' slot of a TDAobj object.", "topics": [ "getOrigData", "getOrigData,PIUMA-getOrigData", "getOrigData,TDAobj-method" ] }, { "page": "getOutcome", "title": "Getter method for the 'outcome' slot of a TDAobj object.", "topics": [ "getOutcome", "getOutcome,PIUMA-getOutcome", "getOutcome,TDAobj-method" ] }, { "page": "getOutcomeFact", "title": "Getter method for the 'outcomeFact' slot of a TDAobj object.", "topics": [ "getOutcomeFact", "getOutcomeFact,PIUMA-getOutcomeFact", "getOutcomeFact,TDAobj-method" ] }, { "page": "getScaledData", "title": "Getter method for the 'scaled_data' slot of a TDAobj object.", "topics": [ "getScaledData", "getScaledData,PIUMA-getScaledData", "getScaledData,TDAobj-method" ] }, { "page": "jaccardMatrix", "title": "Compute the Matrix of Jaccard Indexes", "topics": [ "jaccardMatrix" ] }, { "page": "makeTDAobj", "title": "Import data and generate the TDAobj object", "topics": [ "makeTDAobj" ] }, { "page": "makeTDAobjFromSE", "title": "Import SummarizedExperiment data and generate the TDAobj object", "topics": [ "makeTDAobjFromSE" ] }, { "page": "mapperCore", "title": "Implement the TDA Mapper algorithm on TDAobj", "topics": [ "mapperCore" ] }, { "page": "PIUMA", "title": "PIUMA: Phenotypes Identification Using Mapper from topological data Analysis", "topics": [ "PIUMA" ] }, { "page": "predict_mapper_class", "title": "Predict Mapper Graph Geometry (lightweight)", "topics": [ "predict_mapper_class" ] }, { "page": "setComp", "title": "Setter method for the 'comp' slot of a TDAobj object.", "topics": [ "setComp", "setComp,PIUMA-setComp", "setComp,TDAobj-method" ] }, { "page": "setDfMapper", "title": "Setter method for the 'dfMapper' slot of a TDAobj object.", "topics": [ "setDfMapper", "setDfMapper,PIUMA-setDfMapper", "setDfMapper,TDAobj-method" ] }, { "page": "setDistMat", "title": "Setter method for the 'dist_mat' slot of a TDAobj object.", "topics": [ "setDistMat", "setDistMat,PIUMA-setDistMat", "setDistMat,TDAobj-method" ] }, { "page": "setGraph", "title": "Setter method for the 'graph' slot of a TDAobj object.", "topics": [ "setGraph", "setGraph,PIUMA-setGraph", "setGraph,TDAobj-method" ] }, { "page": "setJacc", "title": "Setter method for the 'jacc' slot of a TDAobj object.", "topics": [ "setJacc", "setJacc,PIUMA-setJacc", "setJacc,TDAobj-method" ] }, { "page": "setNodeDataMat", "title": "Setter method for the 'node_data_mat' slot of a TDAobj object.", "topics": [ "setNodeDataMat", "setNodeDataMat,PIUMA-setNodeDataMat", "setNodeDataMat,TDAobj-method" ] }, { "page": "setOrigData", "title": "Setter method for the 'orig_data' slot of a TDAobj object.", "topics": [ "setOrigData", "setOrigData,PIUMA-setOrigData", "setOrigData,TDAobj-method" ] }, { "page": "setOutcome", "title": "Setter method for the 'outcome' slot of a TDAobj object.", "topics": [ "setOutcome", "setOutcome,PIUMA-setOutcome", "setOutcome,TDAobj-method" ] }, { "page": "setOutcomeFact", "title": "Setter method for the 'outcomeFact' slot of a TDAobj object.", "topics": [ "setOutcomeFact", "setOutcomeFact,PIUMA-setOutcomeFact", "setOutcomeFact,TDAobj-method" ] }, { "page": "setScaledData", "title": "Setter method for the 'scaled_data' slot of a TDAobj object.", "topics": [ "setScaledData", "setScaledData,PIUMA-setScaledData", "setScaledData,TDAobj-method" ] }, { "page": "tda_test_data", "title": "A TDAobj to test the 'PIUMA' package.", "topics": [ "tda_test_data" ] }, { "page": "tdaDfEnrichment", "title": "Add information to TDAobj", "topics": [ "tdaDfEnrichment" ] }, { "page": "TDAobj-class", "title": "The object 'TDAobj'", "topics": [ "TDAobj-class" ] }, { "page": "vascEC_meta", "title": "Example datasets for PIUMA package", "topics": [ "vascEC_meta" ] }, { "page": "vascEC_norm", "title": "We tested PIUMA on a subset of the single-cell RNA Sequencing dataset (GSE:GSE193346 generated and published by Feng et al. (2022) on Nature Communication to demonstrate that distinct transcriptional profiles are present in specific cell types of each heart chambers, which were attributed to have roles in cardiac development. In this tutorial, our aim will be to exploit PIUMA for identifying sub-population of vascular endothelial cells, which can be associated with specific heart developmental stages. The original dataset consisted of three layers of heterogeneity: cell type, stage and zone (i.e., heart chamber). Our testing dataset was obtained by subsetting vascular endothelial cells (cell type) by Seurat object, extracting raw counts and metadata. 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