Package: INDEED 2.21.0

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:Yiming Zuo <[email protected]>, Kian Ghaffari <[email protected]>, Zhenzhi Li <[email protected]>

INDEED_2.21.0.tar.gz
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INDEED.pdf |INDEED.html✨
INDEED/json (API)

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

Peer review:

Bug tracker:https://github.com/ressomlab/indeed/issues

Datasets:

On BioConductor:INDEED-2.19.0(bioc 3.20)INDEED-2.18.0(bioc 3.19)

immunooncologysoftwareresearchfieldbiologicalquestionstatisticalmethoddifferentialexpressionmassspectrometrymetabolomics

5.92 score 4 stars 10 scripts 116 downloads 3 mentions 4 exports 100 dependencies

Last updated 23 days agofrom:c505f8307b. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winOKOct 30 2024
R-4.5-linuxOKOct 30 2024
R-4.4-winOKOct 30 2024
R-4.4-macOKOct 30 2024
R-4.3-winOKOct 30 2024
R-4.3-macOKOct 30 2024

Exports:network_displaynon_partial_corpartial_corselect_rho_partial

Dependencies:askpassbase64encbrewbriobslibcachemcallrclicliprcommonmarkcpp11crayoncredentialscurldescdevtoolsdiffobjdigestdownlitellipsisevaluatefansifastmapfontawesomefsgertghgitcredsglassogluehighrhtmltoolshtmlwidgetshttpuvhttr2igraphinijquerylibjsonliteknitrlaterlatticelifecyclemagrittrMatrixmemoisemimeminiUIopensslpillarpkgbuildpkgconfigpkgdownpkgloadpraiseprettyunitsprocessxprofvispromisespspurrrR6raggrappdirsrcmdcheckRcpprematch2remotesrlangrmarkdownroxygen2rprojrootrstudioapirversionssasssessioninfoshinysourcetoolsstringistringrsyssystemfontstestthattextshapingtibbletinytexurlcheckerusethisutf8vctrsvisNetworkwaldowhiskerwithrxfunxml2xopenxtableyamlzip

INDEED R package for cancer biomarker discovery

Yiming Zuo and Kian Ghaffari

Rendered fromIntroduction_to_INDEED.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2019-09-26
Started: 2018-07-31