| Helper function for subsetting | %like% |
| Align a modification to a peptide sequence | align_modification |
| Align a peptide sequence to a protein sequence | align_peptide |
| A function for evaluating expression differences between two sample sets via the limma algorithm | analysis_counts |
| Analysis tables and plots of expression values | analyze_enrichments |
| Analysis tables and plots of expression values | analyze_expressions |
| Main function for adding annotations to a tidyproteomics data-object | annotate |
| Helper function to convert the data-object into a tibble | as.data.frame.tidyproteomics |
| Helper function to calculate term enrichment | calc_enrichment |
| helper function for normalizing a quantitative table | center |
| Check the integrity of a tidyproteomics data object | check_data |
| Helper function for iterative expression analysis | check_pairs |
| Check the integrity of a tidyproteomics quantitative tibble | check_table |
| Build a tidyproteomics data object | codify |
| Convert peptide quantitative data into protein quantitative data | collapse |
| Helper function to analysis between two expression tests | compute_compexp |
| A helper function for importing peptide table data | data_import |
| Helper function to subset a data frame | down_select |
| Compute protein enrichment | enrichment |
| A function for evaluating term enrichment via Fischer's Exact method | enrichment_fishersexact |
| A function for evaluating term enrichment via GSEA | enrichment_gsea |
| A function for evaluating term enrichment via Wilcoxon Rank Sum | enrichment_wilcoxon |
| Returns the data experimental set up | experimental |
| Main function for adding sample groups | experimental_groups |
| Export the quantitative data from an tidyproteomics data-object | export_analysis |
| Comparative analysis between two expression tests | export_compexp |
| Helper function to export the config file to current project directory | export_config |
| Export the quantitative data from an tidyproteomics data-object | export_quant |
| Summarize the data | expression |
| Calculate expression differences between two-samples | expression_limma |
| A function for evaluating expression differences between two sample sets via the limma algorithm | expression_test |
| Main function for extracting quantitative data from a tidyproteomics data-object | extract |
| Proteolytic digest a parsed fasta list | fasta_digest |
| Get the string defined by the regex | fasta_extract |
| The main function for parsing a fasta file | fasta_parse |
| Proteolytic digest a sequence | fasta_peptides |
| Get/Set the FASTA meta data regex | fasta_regex |
| Calculates the geometric mean of a numeric vector with NAs removed | fgeomean |
| Calculates the mean of a numeric vector with NAs removed | fmean |
| Calculates the median of a numeric vector with NAs removed | fmedian |
| Calculates the minimum of a numeric vector with NAs removed | fmin |
| Calculates the sum of a numeric vector with NAs removed | fsum |
| Helper function to get all accounting terms | get_accountings |
| Helper function to get available terms | get_annotation_terms |
| Helper function to get all annotations for a given term | get_annotations |
| Get the quantitative value names | get_quant_names |
| Helper function to get all sample names | get_sample_names |
| Helper function to get available terms | get_segment |
| Helper function to get all sample names | get_unique_variables |
| Helper function to get available terms | get_variables |
| Create a crc32 hash on a vector | hash_vector |
| Helper function to take the head of a tibble and display as a data.frame | hdf |
| A sample tidyproteomics data object | hela_peptides |
| A sample tidyproteomics data object | hela_proteins |
| Main function for importing data | import |
| A helper function for importing peptide table data | import_extract |
| A helper function for importing peptide table data | import_mbr |
| A helper function for importing peptide table data | import_remove |
| A helper function for importing peptide table data | import_rename |
| A helper function for importing peptide table data | import_split |
| A helper function for importing peptide table data | import_validate |
| Main method for imputing missing values | impute |
| Helper function for calculating imputation stats | impute_ratio |
| Imputes missing values based on the missForest function | impute.randomforest |
| Helper function extracting a subset of proteins | intersect_venn |
| Create a data subset | intersection |
| Inverse Log 2 | invlog2 |
| Helper function Venn and Euler plots | list_venn |
| Load project specific data | load_local |
| match a named vector to string vector | match_vect |
| Meld a tidyproteomics data object into a single table | meld |
| Merge multiple tidyproteomics data-objects | merge |
| Helper function merging normalized data back into the main data-object | merge_quantitative |
| Main function for munging peptide data from an extracted tidyproteomics data-object | munge_identifier |
| Main function for normalizing quantitative data in a tidyproteomics data-object | normalize |
| Normalization function for a tidyproteomics data-object | normalize_limma |
| Normalization function for a tidyproteomics data-object | normalize_linear |
| Normalization function for a tidyproteomics data-object | normalize_loess |
| Normalization function for a tidyproteomics data-object | normalize_median |
| Normalization function for a tidyproteomics data-object | normalize_randomforest |
| Normalization function for a tidyproteomics data-object | normalize_scaled |
| Normalization function for a tidyproteomics data-object | normalize_svm |
| Returns the data transformations | operations |
| Helper function for displaying path to data | path_to_package_data |
| Comparative analysis between two expression tests | plot_compexp |
| Plot the accounting of proteins. peptides, and other counts | plot_counts |
| Plot CVs by abundance | plot_dynamic_range |
| Bubble plot of enrichment values | plot_enrichment |
| GGplot2 extension to plot a Euler diagram | plot_euler |
| Plot a heatmap of quantitative values by sample | plot_heatmap |
| Plot normalized values | plot_normalization |
| Plot PCA values | plot_pca |
| Plot proportional expression values | plot_proportion |
| Visualize mapped sequence data | plot_protein |
| Plot the variation in normalized values | plot_quantrank |
| Helper function for saving plots | plot_save |
| Plot the variation in normalized values | plot_variation_cv |
| Plot the PCA variation in normalized values | plot_variation_pca |
| GGplot2 extension to plot a Venn diagram | plot_venn |
| Volcano plot of expression values | plot_volcano |
| Tidy-Quant data object plot definition | plot.tidyproteomics |
| Tidy-Quant data object print definition | print.tidyproteomics |
| Helper function for printing messages | println |
| Align a peptide data to protein sequences for visualization | protein_map |
| Align a peptide data to protein sequences for visualization | protein_map_munge |
| Read data by format type | read_data |
| A helper function for importing peptide table data | read_mzTab |
| reassign the sample info | reassign |
| Reverse the plot axis for log transformation | reverselog_transformation |
| parallel compute function for randomforest | rf_parallel |
| Remove MBR from the dataset across segments | rm.mbr |
| Store data locally | save_local |
| Write table data locally | save_table |
| Select a normalization method | select_normalization |
| set a named vector | set_vect |
| Display the current annotation data | show_annotations |
| Assess the relative amount of protein contamination | stats_contamination |
| Helper function for displaying data | stats_print |
| Summarize the protein accounting | stats_summary |
| Normalize the column names in a tibble | str_normalize |
| Create a data subset | subset.tidyproteomics |
| Summarize the data | summary.tidyproteomics |
| parallel compute function for randomforest | svm_parallel |
| Helper function to quantitation plots | table_quantrank |
| helper function for having nice colors | theme_palette |
| Tidy-Quant data object print definition | tidyproteomics |
| Helper function to subset a data frame | tidyproteomics_quo |
| Helper function to get a name from the ... | tidyproteomics_quo_name |
| Helper function to summarize the data | tidyproteomics_summary |
| helper function for normalizing quantitative data from a tidyproteomics data-object | transform_factor |
| helper function for normalizing a quantitative table | transform_log2 |
| helper function for normalizing quantitative data from a tidyproteomics data-object | transform_median |
| Helper functio to write data table locally | write_local |
