Introduction | Installation | Load package | Testing dataset | non-partial correlation data analysis function non_partial_cor() | partial correlation data preprocessing function select_rho_partial() | partial correlation data analysis function partial_cor() | Interactive Network Visualization function network_display()
Package: INDEED 2.27.0
Ressom group
INDEED: Interactive Visualization of Integrated Differential Expression and Differential Network Analysis for Biomarker Candidate Selection Package
An R package for integrated differential expression and differential network analysis based on omic data for cancer biomarker discovery. Both correlation and partial correlation can be used to generate differential network to aid the traditional differential expression analysis to identify changes between biomolecules on both their expression and pairwise association levels. A detailed description of the methodology has been published in Methods journal (PMID: 27592383). An interactive visualization feature allows for the exploration and selection of candidate biomarkers.
Authors:
INDEED_2.27.0.tar.gz
INDEED_2.27.0.zip(r-4.7)INDEED_2.27.0.zip(r-4.6)INDEED_2.27.0.zip(r-4.5)
INDEED_2.27.0.tgz(r-4.6-any)INDEED_2.27.0.tgz(r-4.5-any)
INDEED_2.27.0.tar.gz(r-4.7-any)INDEED_2.27.0.tar.gz(r-4.6-any)
INDEED_2.27.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
INDEED/json (API)
| # Install 'INDEED' in R: |
| install.packages('INDEED', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/ressomlab/indeed/issues
Datasets:
- Met_Group_GU - Group label.
- Met_GU - GU cirrhosis (CIRR) and GU Hepatocellular carcinoma (HCC) data.
- Met_name_GU - KEGG ID
- pvalue_M_GU - P-values obtained by differential expression (DE) analysis.
On BioConductor:INDEED-2.27.0(bioc 3.24)INDEED-2.26.0(bioc 3.23)
immunooncologysoftwareresearchfieldbiologicalquestionstatisticalmethoddifferentialexpressionmassspectrometrymetabolomics
Last updated from:094b45e07c. Checks:1 ERROR, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 170 | ||
| linux-devel-x86_64 | OK | 189 | ||
| source / vignettes | OK | 191 | ||
| linux-release-x86_64 | OK | 200 | ||
| macos-release-arm64 | OK | 116 | ||
| macos-oldrel-arm64 | OK | 85 | ||
| windows-devel | OK | 118 | ||
| windows-release | OK | 119 | ||
| windows-oldrel | OK | 113 | ||
| wasm-release | OK | 138 |
Exports:network_displaynon_partial_corpartial_corselect_rho_partial
Dependencies:askpassbase64encbrewbriobslibcachemcallrclicliprcommonmarkcpp11crayoncredentialscurldescdevtoolsdiffobjdigestdownlitellipsisevaluatefansifastmapfontawesomefsgertgitcredsglassogluehighrhtmltoolshtmlwidgetshttpuvhttr2igraphinijquerylibjsonliteknitrlaterlatticelifecyclemagrittrMatrixmemoisemimeminiUIopensslotelpakpillarpkgbuildpkgconfigpkgdownpkgloadpraiseprettyunitsprocessxprofvispromisespspurrrR6raggrappdirsrcmdcheckRcpprlangrmarkdownroxygen2rprojrootrstudioapirversionssasssessioninfoshinysourcetoolsstringisyssystemfontstestthattextshapingtibbletinytexurlcheckerusethisutf8vctrsvisNetworkwaldowhiskerwithrxfunxml2xopenxtableyamlzip
