{ "_id": "6aad6d2d3d719c1f840772af", "Package": "biocohort", "Title": "Cohort Objects for Subjects and Samples in Omics Studies", "Version": "0.1.1", "Authors@R": "c(\nperson(\"Samuel\", \"Bharti\", , \"samuelbharti.io@gmail.com\",\nrole = c(\"aut\", \"cre\", \"cph\"),\ncomment = c(ORCID = \"0000-0003-4190-7058\")),\nperson(\"Barret\", \"Schloerke\", , \"barret@posit.co\", role = \"ths\",\ncomment = c(ORCID = \"0000-0001-9986-114X\")),\nperson(\"Carson\", \"Sievert\", , \"carson@posit.co\", role = \"ths\",\ncomment = c(ORCID = \"0000-0002-4958-2844\")),\nperson(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\"),\ncomment = c(ROR = \"03wc8by49\"))\n)", "Description": "Keeps the subjects, samples, and analysis outputs of a\nstudy in one validated object. It starts from a sample manifest\nwith one row per sample, which is read, checked, and split into\na subject table and a sample map. Species and assay are plain\nvalues in those tables rather than fixed types, so the same\nobject serves any organism and any omics assay. From that\nobject the package writes the sample sheet a pipeline expects,\npairs tumor and normal samples on demand, and records where\neach analysis writes its output so the files can be loaded back\nin by subject or by pair. Manual corrections are kept in an\naudit trail. Results can also be translated across genome\nbuilds or species, with liftover for coordinates and ortholog\nmapping for genes.", "License": "MIT + file LICENSE", "URL": "https://www.samuelbharti.com/biocohort/,\nhttps://github.com/samuelbharti/biocohort", "BugReports": "https://github.com/samuelbharti/biocohort/issues", "Encoding": "UTF-8", "Language": "en-US", "SystemRequirements": "CrossMap (optional, for the CrossMap liftover\nbackend)", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "LazyData": "true", "Config/roxygen2/version": "8.0.0", "NeedsCompilation": "no", "Packaged": { "Date": "2026-09-18 16:51:24 UTC", "User": "root" }, "Author": "Samuel Bharti [aut, cre, cph] (ORCID:\n), Barret Schloerke\n[ths] (ORCID: ), Carson\nSievert [ths] (ORCID: ),\nPosit Software, PBC [cph, fnd] (ROR:\n)", "Maintainer": "Samuel Bharti ", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2026-09-18 11:20:14 UTC", "RemoteUrl": "https://github.com/cran/biocohort", 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in a cohort", "topics": [ "analysis_register" ] }, { "page": "analysis_spec", "title": "Retrieve an analysis specification from registry", "topics": [ "analysis_spec" ] }, { "page": "analysis_spec_new", "title": "Create an AnalysisSpec object", "topics": [ "analysis_spec_new" ] }, { "page": "AnalysisSpec", "title": "S7 AnalysisSpec class", "topics": [ "AnalysisSpec" ] }, { "page": "apply_corrections", "title": "Apply documented corrections to a manifest", "topics": [ "apply_corrections" ] }, { "page": "as_coldata", "title": "Build sample metadata for a count matrix", "topics": [ "as_coldata" ] }, { "page": "check_paths", "title": "Check that a cohort's file paths exist on disk", "topics": [ "check_paths" ] }, { "page": "Cohort", "title": "S7 Cohort class", "topics": [ "Cohort" ] }, { "page": "cohort_contrasts", "title": "Every pairwise contrast between a cohort's groups", "topics": [ "cohort_contrasts" ] }, { "page": "cohort_derive", "title": "Derive a column from cutoffs on an existing numeric column", "topics": [ "cohort_derive" ] }, { "page": "cohort_filter", "title": "Keep a subset of a cohort's subjects or assays", "topics": [ "cohort_filter" ] }, { "page": "cohort_groups", "title": "Group a cohort's subjects by one or more columns", "topics": [ "cohort_groups" ] }, { "page": "cohort_new", "title": "Create a Cohort object", "topics": [ "cohort_new" ] }, { "page": "cohort_qc", "title": "Flag or drop subjects or samples for quality control", "topics": [ "cohort_qc" ] }, { "page": "cohort_read", "title": "Read a cohort saved with cohort_save()", "topics": [ "cohort_read" ] }, { "page": "cohort_save", "title": "Save a cohort to an RDS file", "topics": [ "cohort_save" ] }, { "page": "completeness", "title": "Per-assay sample counts for a cohort", "topics": [ "completeness" ] }, { "page": "corrections_log", "title": "Return the audit table of a corrected manifest", "topics": [ "corrections_log" ] }, { "page": "derive_log", "title": "Read a cohort's derived-column log", "topics": [ "derive_log" ] }, { "page": "ensure_dir", "title": "Create a folder when it is absent", "topics": [ "ensure_dir" ] }, { "page": "example_cohort", "title": "Example Cohort Dataset", "topics": [ "example_cohort" ] }, { "page": "join_metadata", "title": "Add cohort metadata to an analysis object", "topics": [ "join_metadata" ] }, { "page": "liftover_backends", "title": "List registered liftover backends", "topics": [ "liftover_backends" ] }, { "page": "liftover_crossmap", "title": "Liftover backend backed by CrossMap", "topics": [ "liftover_crossmap" ] }, { "page": "liftover_intervals", "title": "Liftover a set of genomic intervals across assemblies or species", "topics": [ "liftover_intervals" ] }, { "page": "liftover_rtracklayer", "title": "Liftover backend backed by rtracklayer", "topics": [ "liftover_rtracklayer" ] }, { "page": "liftover_vcf", "title": "Liftover a VCF of variants with CrossMap (allele-aware)", "topics": [ "liftover_vcf" ] }, { "page": "load_analyses", "title": "Load registered analyses into a cohort from disk", "topics": [ "load_analyses" ] }, { "page": "load_analysis", "title": "Load an analysis's feature table from disk", "topics": [ "load_analysis" ] }, { "page": "manifest_from_wide", "title": "Reshape a wide sample table into a long-format manifest", "topics": [ "manifest_from_wide" ] }, { "page": "ortholog_babelgene", "title": "Ortholog backend backed by babelgene", "topics": [ "ortholog_babelgene" ] }, { "page": "ortholog_backends", "title": "List registered ortholog backends", "topics": [ "ortholog_backends" ] }, { "page": "ortholog_genes", "title": "Map gene-level features to orthologs in another species", "topics": [ "ortholog_genes" ] }, { "page": "orthologize", "title": "Deprecated alias for translate()", "topics": [ "orthologize" ] }, { "page": "project_path", "title": "Build a path under the project root", "topics": [ "project_path" ] }, { "page": "project_root", "title": "Find the project root folder", 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