# Multiplexes Isobaric Mass Tagged-based Kinetics Data for Network Analysis

## Documentation for package ‘XINA’ version 1.6.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

add_legend | add_legend
alluvial_enriched | alluvial_enriched
alluvial_enrichment_tests | alluvial_enrichment_tests
calculate_centrality_scores | calculate_centrality_scores
default_size | default_size
draw_alluvial_plot | draw_alluvial_plot
example_clusters | Randomly generated example datasets for XINA users. A dataset containing the XINA clustering results.
extract_data_column | extract_data_column
find_similar_clusters | find_similar_clusters
generate_count_table | generate_count_table
generate_superset | generate_superset
get_colors | get_colors
get_color_for_nodes | get_color_for_nodes
get_comigrations_by_name | get_comigrations_by_name
get_condition_biased_comigrations | get_condition_biased_comigrations
get_layout | get_layout
get_mTOR_proteins | get_mTOR_proteins
get_random_data | get_random_data
get_stats | get_stats
get_theme_blank | get_theme_blank
get_unknown_ppi_nodes | get_unknown_ppi_nodes
gn | A character vector containing 19,396 human genes This is for the randome data generation of XINA
gn_desc | A character vector containing 19,396 human gene descriptions This is for the randome data generation of XINA
hprd_ppi | Protein-protein interaction resource downloaded from HPRD DB A data frame containing HRPD protein-protein interaction data
length2 | length2
load_previous_results | load_previous_results
make_random_xina_data | make_random_xina_data
mutate_colors | mutate_colors
organize_clusters | organize_clusters
plot_clusters | plot_clusters
plot_clusters_all | plot_clusters_all
plot_condition_compositions | plot_condition_compositions
plot_enrichment_results | plot_enrichment_results
plot_NA | plot_NA
rank_centrality | rank_centrality
string_example | Protein-protein interaction resource downloaded from STRING DB for XINA's example dataset A data frame containing protein-protein interactions
xina_analysis | xina_analysis
xina_clustering | xina_clustering
xina_enrichment | xina_enrichment
xina_plot_all | xina_plot_all
xina_plot_bycluster | xina_plot_bycluster
xina_plot_single | xina_plot_single
xina_result_example | Previously processed xina analysis using XINA's random example data A list containing 'xina_analysis' results