title: "Introduction to the XINA pagkage"author: "Lang Ho Lee, Sasha A. Singh"date: "February 6, 2019"vignette: >%\VignetteEngine{knitr::rmarkdown}%\VignetteEncoding{utf-8}%\VignetteIndexEntry{xina_user_code}output:knitr:::html_vignette:df_print: kabletoc: truenumber_sections: true | 1. Introduction | 1-1. Main contribution | 1-2. Data inputs | 2. XINA websites | 3. XINA installation | 4. Example theoretical dataset | 5. Package features | 5.1 Clustering analysis using model-based clustering or k-means clustering algorithm | 5.2 coregulation analysis | 5.3 Network analysis
Package: XINA 1.31.0
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:
XINA_1.31.0.tar.gz
XINA_1.31.0.zip(r-4.7)XINA_1.31.0.zip(r-4.6)XINA_1.31.0.zip(r-4.5)
XINA_1.31.0.tgz(r-4.6-any)XINA_1.31.0.tgz(r-4.5-any)
XINA_1.31.0.tar.gz(r-4.7-any)XINA_1.31.0.tar.gz(r-4.6-any)
XINA_1.31.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
XINA/json (API)
| # Install 'XINA' in R: |
| install.packages('XINA', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
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-1.31.0(bioc 3.24)XINA-1.30.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
systemsbiologyproteomicsrnaseqnetwork
Last updated from:6b0b4dfde7. Checks:8 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 174 | ||
| linux-devel-x86_64 | WARNING | 226 | ||
| source / vignettes | OK | 206 | ||
| linux-release-x86_64 | WARNING | 182 | ||
| macos-release-arm64 | WARNING | 134 | ||
| macos-oldrel-arm64 | WARNING | 120 | ||
| windows-devel | WARNING | 190 | ||
| windows-release | WARNING | 199 | ||
| windows-oldrel | WARNING | 186 | ||
| wasm-release | OK | 118 |
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:alluvialaskpassbitbit64bitopsblobcachemcaToolschronclicpp11curlDBIfarverfastmapggplot2gluegplotsgridExtragsubfngtablegtoolshashhttrigraphisobandjsonliteKernSmoothlabelinglatticelifecyclemagrittrMatrixmclustmemoisemimeopensslpkgconfigplotrixplyrpngprotoR6RColorBrewerRcpprlangRSQLiteS7scalessqldfSTRINGdbsysvctrsviridisLitewithr
