AnalysisSpec            S7 AnalysisSpec class
Cohort                  S7 Cohort class
Study                   S7 Study class
Subject                 S7 Subject class
TranslationResult       Result of a cross-species or cross-assembly
                        translation
analysis_files          Retrieve analysis file manifests from a cohort
analysis_list           List registered analysis specifications
analysis_register       Register an analysis specification in a cohort
analysis_spec           Retrieve an analysis specification from
                        registry
analysis_spec_new       Create an AnalysisSpec object
apply_corrections       Apply documented corrections to a manifest
as_coldata              Build sample metadata for a count matrix
biocohort-package       biocohort: Subject and Sample Rosters for Omics
                        Studies
check_paths             Check that a cohort's file paths exist on disk
cohort_contrasts        Every pairwise contrast between a cohort's
                        groups
cohort_derive           Derive a column from cutoffs on an existing
                        numeric column
cohort_filter           Keep a subset of a cohort's subjects or assays
cohort_groups           Group a cohort's subjects by one or more
                        columns
cohort_new              Create a Cohort object
cohort_qc               Flag or drop subjects or samples for quality
                        control
cohort_read             Read a cohort saved with cohort_save()
cohort_save             Save a cohort to an RDS file
completeness            Per-assay sample counts for a cohort
corrections_log         Return the audit table of a corrected manifest
derive_log              Read a cohort's derived-column log
ensure_dir              Create a folder when it is absent
example_cohort          Example Cohort Dataset
join_metadata           Add cohort metadata to an analysis object
liftover_backends       List registered liftover backends
liftover_crossmap       Liftover backend backed by CrossMap
liftover_intervals      Liftover a set of genomic intervals across
                        assemblies or species
liftover_rtracklayer    Liftover backend backed by rtracklayer
liftover_vcf            Liftover a VCF of variants with CrossMap
                        (allele-aware)
load_analyses           Load registered analyses into a cohort from
                        disk
load_analysis           Load an analysis's feature table from disk
manifest_from_wide      Reshape a wide sample table into a long-format
                        manifest
ortholog_babelgene      Ortholog backend backed by babelgene
ortholog_backends       List registered ortholog backends
ortholog_genes          Map gene-level features to orthologs in another
                        species
orthologize             Deprecated alias for translate()
project_path            Build a path under the project root
project_root            Find the project root folder
qc_log                  Read a cohort's QC log
read_corrections        Read a corrections table from a file
read_dotenv             Read a dotenv file into the environment
read_manifest           Read and validate a long-format manifest file
read_manifest_csv       Read and validate a long-format manifest CSV
                        file
read_study_yaml         Build a cohort from a study YAML file
register_liftover_backend
                        Register a liftover backend
register_ortholog_backend
                        Register a gene-ortholog backend
sample_pairs            Derive sample pairs from a sample map
sample_sheet            Write a pipeline sample sheet from a cohort
sample_sheet_templates
                        List the built-in sample sheet templates
samples                 Read the sample map of a cohort
study_new               Create a Study object
subject                 Build one Subject from a cohort
subject_new             Create a Subject object
subjects                Read the subject table of a cohort
translate               Translate features (or a whole cohort) across
                        species or assemblies
translation_report      Retrieve per-analysis translation results from
                        a cohort
translation_stats       Summary statistics for a translation
validate_cohort         Validate a Cohort object
validate_manifest       Validate and structure a long-format sample
                        manifest
write_manifest          Write a manifest or a cohort's tables to a
                        delimited file
write_study_yaml        Write a cohort as a study YAML file
