Package index
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MetaProViz-package
MetaProViz
- The MetaProViz package
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alanine_pathways
- alanine_pathways
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biocrates_features
- biocrates_features
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cellular_meta
- cellular_meta
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checkmatch_pk_to_data()
- Check and summarize prior_knowledge-to-MeasuredFeatures relationship
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compare_pk()
- Compare Prior Knowledge Resources and/or Columns within a Single Resource and Generate an UpSet Plot
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count_id()
- Count Entries and Generate a Histogram Plot for a Specified Column
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dma()
- This function allows you to perform differential metabolite analysis to obtain a Log2FC, pval, padj and tval comparing two or multiple conditions.
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equivalent_features
- equivalent_features
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equivalent_id()
- Find additional potential IDs for "kegg", "pubchem", "chebi", "hmdb"
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gaude_pathways
- gaude_pathways
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hallmarks
- hallmarks
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intracell_dma
- intracell_dma
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intracell_raw
- intracell_raw
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make_gene_metab_set()
- Function to add metabolite HMDB IDs to existing genesets based on cosmosR prior knowledge
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mapping_ambiguity()
- Create Mapping Ambiguities between two ID types
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mca_core()
- This script performs metabolite clustering analysis and computes clusters of metabolites based on regulatory rules between Intracellular and culture media metabolomics (core experiment).
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mca_core_rules
- mca_core_rules
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mca_twocond_rules
- mca_twocond_rules
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medium_raw
- medium_raw
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meta_pk()
- Meta prior-knowledge
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metadata_analysis()
- This function performs a PCA analysis on the input data and combines it with the sample metadata to perform an ANOVA test to identify significant differences between the groups.
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metaproviz_config_path()
- Current config file path of MetaProViz
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metaproviz_load_config()
- Load the package configuration from a config file
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metaproviz_log()
- Browse the current MetaProViz log file
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metaproviz_logfile()
- Path to the current MetaProViz log file
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metaproviz_reset_config()
- Restore the built-in default values of all config parameters of MetaProViz
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metaproviz_save_config()
- Save the current package configuration
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metaproviz_set_loglevel()
- Sets the log level for the package logger
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metsigdb_chemicalclass()
- Prior Knowledge Import
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metsigdb_kegg()
- KEGG
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metsigdb_metalinks()
- Annotated metabolite-protein interactions from MetalinksDB
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pool_estimation()
- Find metabolites with high variability across total pool samples
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processing()
- Modularised Normalization: 80%-filtering rule, total-ion count normalization, missing value imputation and Outlier Detection: HotellingT2.
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replicate_sum()
- Merges the analytical replicates of an experiment
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standard_ora()
- Uses enricher to run ORA on the differential metabolites (DM) using a pathway list
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tissue_dma
- tissue_dma
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tissue_dma_old
- tissue_dma_old
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tissue_dma_young
- tissue_dma_young
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tissue_meta
- Tissue_Metadata
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tissue_norm
- tissue_norm
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tissue_tvn_proteomics
- tissue_tvn_proteomics
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tissue_tvn_rnaseq
- tissue_tvn_rnaseq
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translate_id()
- Translate IDs to/from KEGG, PubChem, Chebi, HMDB
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viz_heatmap()
- Heatmap visualization
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viz_pca()
- This script allows you to perform PCA plot visualization using the results of the MetaProViz analysis PCA plot visualization
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viz_superplot()
- This script allows you to perform different visualizations (bar, box, violin plots) using the results of the MetaProViz analysis Bar, Box or Violin plot in Superplot style visualization
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viz_volcano()
- This script allows you to perform different data visualizations using the results of the MetaProViz analysis Volcano plot visualization