Man pages for mensxmachina/BioDataome
Functions used to preprocess datasets stored in BioDataome
| compareDsetList | Column wise comparison of a dataset to a list of datasets. |
| compareDsets | Column wise comparison of two datasets This function finds... |
| controlSamples | Discover control samples from phenotype data in GEO |
| curateGSE | Run all steps to download, preprocess and annotate a GEO... |
| curateRecountRNASeq | Run all steps to download, preprocess and annotate an RNASeq... |
| diseasetoChildrenNodes | Map a Disease Ontology (D-O) term to the first children nodes... |
| diseasetoParentNodes | Map a Disease Ontology (D-O) term to the parent nodes in D-O |
| downloadPhenotype | Download series matrices from GEO for a given study |
| downloadPhenotypePlatform | Download series matrix from GEO for a given study and... |
| downloadRaw | Download raw files from GEO for a given study Example:... |
| downloadRecount | Download gene-level RangedSummarizedExperiment data from... |
| entrezIDtoGSE | Find all GSE ids for a given Entrez query Example: query GEO... |
| GSEmetadata | Create sample phenotype metadata of a GEO dataset including... |
| GSEtoDisease | Annotate a study (GSE) with a disease term from the Disease... |
| GSEtoDiseaseGEO | Annotate a study (GSE) with a disease term from the Disease... |
| preprocessGEO | Preprocess CEL files with SCAN |
| preprocessGEOMethylation | Preprocess IDAT files from Illumina HumanMethylation450... |
| recountIDtoGSE | Map a recount dataset ID to GSE ID |
