Package index • MotrpacHumanPreSuspensionAnalysis

All functions

CAMERA_RESULTS: CAMERA enrichment analysis results
CONTRAST_CONVERTER: Contrast Converter
COVARIATES_FILE: Covariates used for statistical analysis
ADIPOSE_METAB_DA ADIPOSE_PROT_PH_DA ADIPOSE_PROT_PR_DA ADIPOSE_TRNSCRPT_DA BLOOD_METAB_DA BLOOD_PROT_OL_DA BLOOD_TRNSCRPT_DA MUSCLE_METAB_DA MUSCLE_PROT_PH_DA MUSCLE_PROT_PR_DA MUSCLE_TRNSCRPT_DA: Differential Analysis Results
FCM_CLUSTERS FCM_CAMERA FCM_ORA: Fuzzy c-means clustering and enrichment analysis results
HUMAN_ACUTE_TIMEPOINT_COLORS: Color scheme for acute exercise timepoints
HUMAN_EXERCISE_GROUP_COLORS: Color scheme for exercise group differentiation
HUMAN_FEATURE_TO_GENE: Human Feature to Gene Conversion Table
HUMAN_OME_COLORS: Color scheme for molecular modality (omics layer) differentiation
HUMAN_SEX_COLORS: Color scheme for sex-based differentiation
HUMAN_TISSUE_ABBR: Tissue abbreviations for compact figure annotation
HUMAN_TISSUE_COLORS: Color scheme for tissue-based differentiation
METABOLOMICS_CVS: Metabolite Coefficients of Variation
MOLECULAR_SIGNATURES: Molecular pathway signatures
OME_TISSUE_CODE: Tissue codes relevant for a given ome
OUTLIERS: List of outliers designated by the Pre-CAWG working group.
SET_TO_ID: Gene set ID to pathway name mapping
SPLICING_DA: Differential Alternative Splicing Results
ADIPOSE_EPIGEN_METHYLCAP_SEQ_SUM_STATS ADIPOSE_METAB_T_ACOA_SUM_STATS ADIPOSE_METAB_T_AMINES_SUM_STATS ADIPOSE_METAB_T_TCA_SUM_STATS ADIPOSE_METAB_T_NUC_SUM_STATS ADIPOSE_METAB_T_KA_SUM_STATS ADIPOSE_METAB_T_OXYLIPNEG_SUM_STATS ADIPOSE_METAB_U_HILICPOS_SUM_STATS ADIPOSE_METAB_U_IONPNEG_SUM_STATS ADIPOSE_METAB_U_LRPNEG_SUM_STATS ADIPOSE_METAB_U_LRPPOS_SUM_STATS ADIPOSE_METAB_U_RPNEG_SUM_STATS ADIPOSE_METAB_U_RPPOS_SUM_STATS ADIPOSE_PROT_PH_SUM_STATS ADIPOSE_PROT_PR_SUM_STATS ADIPOSE_TRANSCRIPT_RNA_SEQ_SUM_STATS BLOOD_EPIGEN_METHYLCAP_SEQ_SUM_STATS BLOOD_METAB_T_AMINES_SUM_STATS BLOOD_METAB_T_TCA_SUM_STATS BLOOD_METAB_T_CONV_SUM_STATS BLOOD_METAB_T_OXYLIPNEG_SUM_STATS BLOOD_METAB_U_HILICPOS_SUM_STATS BLOOD_METAB_U_IONPNEG_SUM_STATS BLOOD_METAB_U_LRPNEG_SUM_STATS BLOOD_METAB_U_LRPPOS_SUM_STATS BLOOD_METAB_U_RPNEG_SUM_STATS BLOOD_METAB_U_RPPOS_SUM_STATS BLOOD_PROT_OL_SUM_STATS BLOOD_TRANSCRIPT_RNA_SEQ_SUM_STATS BLOOD_EPIGEN_ATAC_SEQ_SUM_STATS MUSCLE_EPIGEN_METHYLCAP_SEQ_SUM_STATS MUSCLE_METAB_T_AMINES_SUM_STATS MUSCLE_METAB_T_TCA_SUM_STATS MUSCLE_METAB_T_NUC_SUM_STATS MUSCLE_METAB_T_OXYLIPNEG_SUM_STATS MUSCLE_METAB_U_HILICPOS_SUM_STATS MUSCLE_METAB_U_IONPNEG_SUM_STATS MUSCLE_METAB_U_LRPNEG_SUM_STATS MUSCLE_METAB_U_LRPPOS_SUM_STATS MUSCLE_METAB_U_RPNEG_SUM_STATS MUSCLE_METAB_U_RPPOS_SUM_STATS MUSCLE_PROT_PH_SUM_STATS MUSCLE_PROT_PR_SUM_STATS MUSCLE_TRANSCRIPT_RNA_SEQ_SUM_STATS MUSCLE_EPIGEN_ATAC_SEQ_SUM_STATS: Summary Statistics by Tissue, Assay, and Platform
UTORONTO_TFs: Pre-specified transcription Factors from the UToronto dataset
check_package_installation(): Check package installation
load_DA_from_AWS(): Load Epigenomic Differential Analysis Results from AWS
load_differential_analysis(): Load Differential Analysis Results
load_summary_stats(): Load Summary Statistics for Normalized Expression Data
metab_only_list(): List the Metabolomics Platforms
ome_available_list(): List All Omes
plot_cluster_enrichment(): Bubble heatmap of CAMERA-PR or ORA results from fuzzy c-means clustering
plot_cmeans(): Save a Plot of Fuzzy C-Means Cluster Trajectories
plot_enrich_heatmap(): Create a bubble heatmap of molecular signatures from CAMERA-PR or PTM-SEA results
plot_feature_heatmap(): Create a heatmap of select features or a choice pathway.
plot_precovid_cca(): canCor analysis cor correlation to principal components
plot_precovid_pca(): Principal component analysis for the pre-cawg group
plot_single_feature(): Single feature plot function
run_ORA(): Over-Representation Analysis (ORA)
run_SCION(): @title SCION implementation for preCAWG. Combines preprocessing and network inference into one function
run_cameraPR(): Wrapper for CAMERA-PR
run_cluster_ORA(): Analyze Fuzzy C-means Clustering Results with ORA
run_cluster_cameraPR(): Analyze Fuzzy C-Means Clustering Results with CAMERA-PR
run_cmeans(): Fuzzy C-Means (FCM) Clustering
scion_run_cmeans(): Clustering for the scion function
tissue_available_list(): List the Available Tissues