Package: lilikoi 2.1.1

lilikoi: Metabolomics Personalized Pathway Analysis Tool

A comprehensive analysis tool for metabolomics data. It consists a variety of functional modules, including several new modules: a pre-processing module for normalization and imputation, an exploratory data analysis module for dimension reduction and source of variation analysis, a classification module with the new deep-learning method and other machine-learning methods, a prognosis module with cox-PH and neural-network based Cox-nnet methods, and pathway analysis module to visualize the pathway and interpret metabolite-pathway relationships. References: H. Paul Benton <http://www.metabolomics-forum.com/index.php?topic=281.0> Jeff Xia <https://github.com/cangfengzhe/Metabo/blob/master/MetaboAnalyst/website/name_match.R> Travers Ching, Xun Zhu, Lana X. Garmire (2018) <doi:10.1371/journal.pcbi.1006076>.

Authors:Xinying Fang [aut], Yu Liu [aut], Zhijie Ren [aut], Fadhl Alakwaa [aut], Sijia Huang [aut], Lana Garmire [aut, cre]

lilikoi_2.1.1.tar.gz
lilikoi_2.1.1.zip(r-4.5)lilikoi_2.1.1.zip(r-4.4)lilikoi_2.1.1.zip(r-4.3)
lilikoi_2.1.1.tgz(r-4.4-any)lilikoi_2.1.1.tgz(r-4.3-any)
lilikoi_2.1.1.tar.gz(r-4.5-noble)lilikoi_2.1.1.tar.gz(r-4.4-noble)
lilikoi_2.1.1.tgz(r-4.4-emscripten)lilikoi_2.1.1.tgz(r-4.3-emscripten)
lilikoi.pdf |lilikoi.html✨
lilikoi/json (API)
NEWS

Peer review:

On CRAN:

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

11 exports 1 stars 0.49 score 205 dependencies 1 mentions 14 scripts 322 downloads

Last updated 2 years agofrom:1caf63620a. Checks:OK: 7. Indexed: yes.

Exports:lilikoi.explrlilikoi.featuresSelectionlilikoi.KEGGplotlilikoi.Loaddatalilikoi.machine_learninglilikoi.meta_pathlilikoi.MetaTOpathwaylilikoi.PDSfunlilikoi.preproc_knnlilikoi.preproc_normlilikoi.prognosis

Dependencies:abindAnnotationDbiaskpassbackportsbase64encbase64urlBiobaseBiocGenericsBiostringsbitbit64bitopsblobbootbroomcachemcarcarDatacaretcaToolsclasscliclockclustercodetoolscolorspacecommonmarkcorpcorcorrplotcowplotcpp11crayoncurldata.tableDBIDerivdiagramdigestdoBydoParalleldoSNOWdplyre1071evaluateexactRankTestsfansifarverfastmapforeachfsfuturefuture.applygbmgenericsGenomeInfoDbGenomeInfoDbDataggplot2ggpubrggrepelggsciggsignifggtextglmnetglobalsgluegowergplotsgraphgridExtragridtextgtablegtoolsh2ohardhatherehighrhtmltoolshttrimputeinfotheoipredIRangesIRdisplayIRkernelisobanditeratorsjpegjsonliteKEGGgraphKEGGRESTKernSmoothkm.ciKMsurvknitrlabelinglatticelavalifecyclelimmalistenvlme4lubridateM3CmagrittrmarkdownMASSMatrixmatrixcalcMatrixModelsmaxstatmemoiseMetricsmgcvmicrobenchmarkmimeminqaMLmetricsModelMetricsmodelrmunsellmvtnormnlmenloptrnnetnumDerivopensslorg.Hs.eg.dbparallellypathviewpbdZMQpbkrtestpillarpkgconfigplogrplyrpngpolynompreprocessCoreprincurvepROCprodlimprogressrproxypurrrquantregR6rappdirsRColorBrewerRcppRcppEigenRcppTOMLRCurlRCy3recipesreprreshapereshape2reticulateRgraphvizrJavaRJSONIOrlangROCRrpartrprojrootRSpectraRSQLiterstatixRtsneRWekaRWekajarsS4VectorsscalesshapesnowSparseMSQUAREMstatmodstringistringrsurvivalsurvminersurvMiscsystibbletidyrtidyselecttimechangetimeDatetzdbUCSC.utilsumaputf8uuidvctrsviridisLitewithrxfunXMLxml2xtableXVectoryamlzlibbioczoo