Package index • MotrpacRatTraining6moData

Metadata

Phenotypic data

PHENO: Phenotypic data

Ome-specific sample metadata

ATAC_META: ATAC-seq metadata and QC

IMMUNO_META: Multiplexed immunoassay metadata and QC

METHYL_META: RRBS metadata and QC

PHOSPHO_META PROT_META ACETYL_META UBIQ_META: Proteomics sample-level metadata

TRNSCRPT_META: RNA-seq metadata and QC

Sample-level molecular data

Raw sample-level data

ATAC_RAW_COUNTS: ATAC-seq raw counts

METHYL_RAW_COUNTS: RRBS raw counts

TRNSCRPT_ADRNL_RAW_COUNTS TRNSCRPT_BAT_RAW_COUNTS TRNSCRPT_BLOOD_RAW_COUNTS TRNSCRPT_COLON_RAW_COUNTS TRNSCRPT_CORTEX_RAW_COUNTS TRNSCRPT_HEART_RAW_COUNTS TRNSCRPT_HIPPOC_RAW_COUNTS TRNSCRPT_HYPOTH_RAW_COUNTS TRNSCRPT_KIDNEY_RAW_COUNTS TRNSCRPT_LIVER_RAW_COUNTS TRNSCRPT_LUNG_RAW_COUNTS TRNSCRPT_OVARY_RAW_COUNTS TRNSCRPT_SKMGN_RAW_COUNTS TRNSCRPT_SKMVL_RAW_COUNTS TRNSCRPT_SMLINT_RAW_COUNTS TRNSCRPT_SPLEEN_RAW_COUNTS TRNSCRPT_TESTES_RAW_COUNTS TRNSCRPT_VENACV_RAW_COUNTS TRNSCRPT_WATSC_RAW_COUNTS: RNA-seq raw counts

METHYL_RAW_DATA: RRBS raw data

Normalized sample-level data

ACETYL_HEART_NORM_DATA ACETYL_LIVER_NORM_DATA: Normalized protein acetylation data

ATAC_NORM_DATA: Normalized ATAC-seq data

METHYL_NORM_DATA: Normalized DNA methylation data

PHOSPHO_CORTEX_NORM_DATA PHOSPHO_SKMGN_NORM_DATA PHOSPHO_HEART_NORM_DATA PHOSPHO_KIDNEY_NORM_DATA PHOSPHO_LUNG_NORM_DATA PHOSPHO_LIVER_NORM_DATA PHOSPHO_WATSC_NORM_DATA: Normalized protein phosphorylation data

PROT_CORTEX_NORM_DATA PROT_SKMGN_NORM_DATA PROT_HEART_NORM_DATA PROT_KIDNEY_NORM_DATA PROT_LUNG_NORM_DATA PROT_LIVER_NORM_DATA PROT_WATSC_NORM_DATA: Normalized protein expression data

TRAINING_REGULATED_NORM_DATA TRAINING_REGULATED_NORM_DATA_NO_OUTLIERS: Normalized data for training-regulated features

TRNSCRPT_BLOOD_NORM_DATA TRNSCRPT_HIPPOC_NORM_DATA TRNSCRPT_CORTEX_NORM_DATA TRNSCRPT_HYPOTH_NORM_DATA TRNSCRPT_SKMGN_NORM_DATA TRNSCRPT_SKMVL_NORM_DATA TRNSCRPT_HEART_NORM_DATA TRNSCRPT_KIDNEY_NORM_DATA TRNSCRPT_ADRNL_NORM_DATA TRNSCRPT_COLON_NORM_DATA TRNSCRPT_SPLEEN_NORM_DATA TRNSCRPT_TESTES_NORM_DATA TRNSCRPT_OVARY_NORM_DATA TRNSCRPT_VENACV_NORM_DATA TRNSCRPT_LUNG_NORM_DATA TRNSCRPT_SMLINT_NORM_DATA TRNSCRPT_LIVER_NORM_DATA TRNSCRPT_BAT_NORM_DATA TRNSCRPT_WATSC_NORM_DATA: Normalized RNA-seq data

UBIQ_HEART_NORM_DATA UBIQ_LIVER_NORM_DATA: Normalized protein ubiquitynation data

ATAC_HIPPOC_NORM_DATA_05FDR ATAC_SKMGN_NORM_DATA_05FDR ATAC_HEART_NORM_DATA_05FDR ATAC_KIDNEY_NORM_DATA_05FDR ATAC_LUNG_NORM_DATA_05FDR ATAC_LIVER_NORM_DATA_05FDR ATAC_BAT_NORM_DATA_05FDR ATAC_WATSC_NORM_DATA_05FDR: Normalized ATAC-seq data for training-regulated features

METHYL_HIPPOC_NORM_DATA_05FDR METHYL_SKMGN_NORM_DATA_05FDR METHYL_HEART_NORM_DATA_05FDR METHYL_KIDNEY_NORM_DATA_05FDR METHYL_LUNG_NORM_DATA_05FDR METHYL_LIVER_NORM_DATA_05FDR METHYL_BAT_NORM_DATA_05FDR METHYL_WATSC_NORM_DATA_05FDR: Normalized DNA methylation data for training-regulated features

IMMUNO_NORM_DATA_FLAT: Combined immunoassay data used for visualization

METAB_NORM_DATA_FLAT: Combined metabolomics data used for visualization

IMMUNO_NORM_DATA_NESTED: Processed immunoassay data used for differential analysis

METAB_NORM_DATA_NESTED: Processed metabolomics data used for differential analysis

Sample outliers

OUTLIERS: Sample outliers

Differential analysis results

TRAINING_REGULATED_FEATURES: Training-regulated features

ATAC_DA: Differential analysis of ATAC-seq data

IMMUNO_PLASMA_DA IMMUNO_HIPPOC_DA IMMUNO_CORTEX_DA IMMUNO_ADRNL_DA IMMUNO_TESTES_DA IMMUNO_OVARY_DA IMMUNO_SKMGN_DA IMMUNO_BAT_DA IMMUNO_WATSC_DA IMMUNO_COLON_DA IMMUNO_SMLINT_DA IMMUNO_LIVER_DA IMMUNO_SKMVL_DA IMMUNO_HEART_DA IMMUNO_KIDNEY_DA IMMUNO_SPLEEN_DA IMMUNO_LUNG_DA: Differential analysis of multiplexed immunoassays

METAB_PLASMA_DA METAB_HIPPOC_DA METAB_CORTEX_DA METAB_HYPOTH_DA METAB_SKMGN_DA METAB_SKMVL_DA METAB_HEART_DA METAB_KIDNEY_DA METAB_ADRNL_DA METAB_COLON_DA METAB_SPLEEN_DA METAB_TESTES_DA METAB_OVARY_DA METAB_VENACV_DA METAB_LUNG_DA METAB_SMLINT_DA METAB_LIVER_DA METAB_BAT_DA METAB_WATSC_DA: Differential analysis of merged metabolomics datasets

METHYL_DA: Differential analysis results of RRBS data

PROT_CORTEX_DA PROT_SKMGN_DA PROT_HEART_DA PROT_KIDNEY_DA PROT_LUNG_DA PROT_LIVER_DA PROT_WATSC_DA PHOSPHO_CORTEX_DA PHOSPHO_SKMGN_DA PHOSPHO_HEART_DA PHOSPHO_KIDNEY_DA PHOSPHO_LUNG_DA PHOSPHO_LIVER_DA PHOSPHO_WATSC_DA ACETYL_HEART_DA ACETYL_LIVER_DA UBIQ_HEART_DA UBIQ_LIVER_DA: Differential analysis of proteomics datasets

TRAINING_DA: Training differential analysis results

TRNSCRPT_BLOOD_DA TRNSCRPT_HIPPOC_DA TRNSCRPT_CORTEX_DA TRNSCRPT_HYPOTH_DA TRNSCRPT_SKMGN_DA TRNSCRPT_SKMVL_DA TRNSCRPT_HEART_DA TRNSCRPT_KIDNEY_DA TRNSCRPT_ADRNL_DA TRNSCRPT_COLON_DA TRNSCRPT_SPLEEN_DA TRNSCRPT_TESTES_DA TRNSCRPT_OVARY_DA TRNSCRPT_VENACV_DA TRNSCRPT_LUNG_DA TRNSCRPT_SMLINT_DA TRNSCRPT_LIVER_DA TRNSCRPT_BAT_DA TRNSCRPT_WATSC_DA: Differential analysis of RNA-seq datasets

METAB_ADRNL_DA_METAREG METAB_BAT_DA_METAREG METAB_COLON_DA_METAREG METAB_CORTEX_DA_METAREG METAB_HEART_DA_METAREG METAB_HIPPOC_DA_METAREG METAB_HYPOTH_DA_METAREG METAB_KIDNEY_DA_METAREG METAB_LIVER_DA_METAREG METAB_LUNG_DA_METAREG METAB_OVARY_DA_METAREG METAB_PLASMA_DA_METAREG METAB_SKMGN_DA_METAREG METAB_SKMVL_DA_METAREG METAB_SMLINT_DA_METAREG METAB_SPLEEN_DA_METAREG METAB_TESTES_DA_METAREG METAB_VENACV_DA_METAREG METAB_WATSC_DA_METAREG: Meta-regression of metabolomics differential analysis results

Bayesian graphical analysis

Inputs

REPFDR_INPUTS: repfdr inputs

Outputs

GRAPH_STATES: repfdr state assignments

GRAPH_COMPONENTS: Graph components

REPFDR_RES: repfdr results

Pathway enrichment analysis

Inputs

PATHWAY_PARENTS: KEGG and Reactome parent pathways

GENE_UNIVERSES: Gene-centric universes

Results

GRAPH_PW_ENRICH: Graph pathway enrichment results

Mappings

Feature mapping

FEATURE_TO_GENE: Feature-to-gene map

FEATURE_TO_GENE_FILT: Filtered feature-to-gene map

REPEATED_FEATURES: Repeated feature info

RAT_TO_HUMAN_GENE: Rat-to-human gene ortholog map

RAT_TO_HUMAN_PHOSPHO: Rat-to-human phosphosite map

METAB_FEATURE_ID_MAP: Metabolite feature IDs and metadata

ACETYL_FEATURE_ANNOT: Protein acetylation feature annotation

ATAC_FEATURE_ANNOT: ATAC-seq feature annotation

METHYL_FEATURE_ANNOT: RRBS feature annotation

PHOSPHO_FEATURE_ANNOT: Protein phosphorylation feature annotation

PROT_FEATURE_ANNOT: Global protein expression feature annotation

TRNSCRPT_FEATURE_ANNOT: Transcriptomics gene annotation

UBIQ_FEATURE_ANNOT: Protein ubiquitination feature annotation

Abbreviations

ASSAY_ABBREV_TO_CODE: Assay abbreviation-to-code mapping

ASSAY_ABBREV: Assay or "ome" abbreviations

ASSAY_CODE_TO_ABBREV: Assay code-to-abbreviation mapping

TISSUE_ABBREV_TO_CODE: Tissue abbreviation-to-code mapping

TISSUE_ABBREV: Tissue abbreviations

TISSUE_CODE_TO_ABBREV: Tissue code-to-abbreviation mapping

Colors and orders for plotting

ASSAY_COLORS: Assay colors

ASSAY_ORDER: Assay order

GROUP_COLORS: Intervention group colors

SEX_COLORS: Sex colors

TISSUE_COLORS: Tissue colors

TISSUE_ORDER: Tissue order