Package: XINA 1.25.0

Lang Ho Lee

XINA: Multiplexes Isobaric Mass Tagged-based Kinetics Data for Network Analysis

The aim of XINA is to determine which proteins exhibit similar patterns within and across experimental conditions, since proteins with co-abundance patterns may have common molecular functions. XINA imports multiple datasets, tags dataset in silico, and combines the data for subsequent subgrouping into multiple clusters. The result is a single output depicting the variation across all conditions. XINA, not only extracts coabundance profiles within and across experiments, but also incorporates protein-protein interaction databases and integrative resources such as KEGG to infer interactors and molecular functions, respectively, and produces intuitive graphical outputs.

Authors:Lang Ho Lee <[email protected]> and Sasha A. Singh <[email protected]>

XINA_1.25.0.tar.gz
XINA_1.25.0.zip(r-4.5)XINA_1.25.0.zip(r-4.4)XINA_1.25.0.zip(r-4.3)
XINA_1.25.0.tgz(r-4.4-any)XINA_1.25.0.tgz(r-4.3-any)
XINA_1.25.0.tar.gz(r-4.5-noble)XINA_1.25.0.tar.gz(r-4.4-noble)
XINA_1.25.0.tgz(r-4.4-emscripten)XINA_1.25.0.tgz(r-4.3-emscripten)
XINA.pdf |XINA.html✨
XINA/json (API)
NEWS

# Install 'XINA' in R:
install.packages('XINA', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • example_clusters - Randomly generated example datasets for XINA users. A dataset containing the XINA clustering results.
  • 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
  • string_example - Protein-protein interaction resource downloaded from STRING DB for XINA's example dataset A data frame containing protein-protein interactions
  • xina_result_example - Previously processed xina analysis using XINA's random example data A list containing 'xina_analysis' results

On BioConductor:XINA-1.25.0(bioc 3.21)XINA-1.24.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

systemsbiologyproteomicsrnaseqnetwork

4.30 score 3 scripts 246 downloads 2 mentions 18 exports 64 dependencies

Last updated 23 days agofrom:19afdece24. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 19 2024
R-4.5-winOKNov 19 2024
R-4.5-linuxOKNov 19 2024
R-4.4-winOKNov 19 2024
R-4.4-macOKNov 19 2024
R-4.3-winOKNov 19 2024
R-4.3-macOKNov 19 2024

Exports:alluvial_enricheddraw_alluvial_plotget_comigrations_by_nameget_condition_biased_comigrationsget_unknown_ppi_nodesload_previous_resultsmake_random_xina_datamutate_colorsplot_clustersplot_clusters_allplot_condition_compositionsplot_enrichment_resultsxina_analysisxina_clusteringxina_enrichmentxina_plot_allxina_plot_byclusterxina_plot_single

Dependencies:alluvialaskpassbitbit64bitopsblobcachemcaToolschronclicolorspacecpp11curlDBIfansifarverfastmapggplot2gluegplotsgridExtragsubfngtablegtoolshashhttrigraphisobandjsonliteKernSmoothlabelinglatticelifecyclemagrittrMASSMatrixmclustmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrplotrixplyrpngprotoR6RColorBrewerRcpprlangRSQLitescalessqldfSTRINGdbsystibbleutf8vctrsviridisLitewithr

xina_user_code

Rendered fromxina_user_code.Rmdusingknitr::rmarkdownon Nov 19 2024.

Last update: 2019-02-06
Started: 2018-08-20

Readme and manuals

Help Manual

Help pageTopics
add_legendadd_legend
alluvial_enrichedalluvial_enriched
alluvial_enrichment_testsalluvial_enrichment_tests
calculate_centrality_scorescalculate_centrality_scores
default_sizedefault_size
draw_alluvial_plotdraw_alluvial_plot
Randomly generated example datasets for XINA users. A dataset containing the XINA clustering results.example_clusters
extract_data_columnextract_data_column
find_similar_clustersfind_similar_clusters
generate_count_tablegenerate_count_table
generate_supersetgenerate_superset
get_color_for_nodesget_color_for_nodes
get_colorsget_colors
get_comigrations_by_nameget_comigrations_by_name
get_condition_biased_comigrationsget_condition_biased_comigrations
get_layoutget_layout
get_mTOR_proteinsget_mTOR_proteins
get_random_dataget_random_data
get_statsget_stats
get_theme_blankget_theme_blank
get_unknown_ppi_nodesget_unknown_ppi_nodes
A character vector containing 19,396 human genes This is for the randome data generation of XINAgn
A character vector containing 19,396 human gene descriptions This is for the randome data generation of XINAgn_desc
Protein-protein interaction resource downloaded from HPRD DB A data frame containing HRPD protein-protein interaction datahprd_ppi
length2length2
load_previous_resultsload_previous_results
make_random_xina_datamake_random_xina_data
mutate_colorsmutate_colors
organize_clustersorganize_clusters
plot_clustersplot_clusters
plot_clusters_allplot_clusters_all
plot_condition_compositionsplot_condition_compositions
plot_enrichment_resultsplot_enrichment_results
plot_NAplot_NA
rank_centralityrank_centrality
Protein-protein interaction resource downloaded from STRING DB for XINA's example dataset A data frame containing protein-protein interactionsstring_example
xina_analysisxina_analysis
xina_clusteringxina_clustering
xina_enrichmentxina_enrichment
xina_plot_allxina_plot_all
xina_plot_byclusterxina_plot_bycluster
xina_plot_singlexina_plot_single
Previously processed xina analysis using XINA's random example data A list containing 'xina_analysis' resultsxina_result_example