Package: MPAC 1.7.0

Peng Liu

MPAC: Multi-omic Pathway Analysis of Cells

Multi-omic Pathway Analysis of Cells (MPAC), integrates multi-omic data for understanding cellular mechanisms. It predicts novel patient groups with distinct pathway profiles as well as identifying key pathway proteins with potential clinical associations. From CNA and RNA-seq data, it determines genes’ DNA and RNA states (i.e., repressed, normal, or activated), which serve as the input for PARADIGM to calculate Inferred Pathway Levels (IPLs). It also permutes DNA and RNA states to create a background distribution to filter IPLs as a way to remove events observed by chance. It provides multiple methods for downstream analysis and visualization.

Authors:Peng Liu [aut, cre], Paul Ahlquist [aut], Irene Ong [aut], Anthony Gitter [aut]

MPAC_1.7.0.tar.gz
MPAC_1.7.0.zip(r-4.7-any)MPAC_1.7.0.zip(r-4.6-any)MPAC_1.7.0.zip(r-4.5-any)
MPAC_1.7.0.tgz(r-4.6-any)MPAC_1.7.0.tgz(r-4.5-any)
MPAC_1.7.0.tar.gz(r-4.7-any)MPAC_1.7.0.tar.gz(r-4.6-any)
MPAC_1.7.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
MPAC/json (API)

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

Bug tracker:https://github.com/pliu55/mpac/issues

On BioConductor:MPAC-1.7.0(bioc 3.24)MPAC-1.6.0(bioc 3.23)

softwaretechnologysequencingrnaseqsurvivalclusteringimmunooncology

3.30 score 7 scripts 275 downloads 20 exports 160 dependencies

Last updated from:e25384ace4. Checks:7 WARNING, 2 ERROR, 1 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING236
linux-develERROR531
source / vignettesERROR605
linux-releaseWARNING446
macos-releaseWARNING286
macos-oldrelWARNING301
windows-develWARNING308
windows-releaseWARNING357
windows-oldrelWARNING292
wasm-releaseOK198

Exports:clSampcolPermIPLcolRealIPLconMtffltByPermgetSignifOvrOnClovrGMTpltConMtfpltMtfPrtIPLpltNeiSttpltOvrHmpltSttKMppCnInpppPermInpppRealInpppRnaInpppRunPrdrunPermPrdrunPrdsubNtw

Dependencies:abindassortheadbackportsbase64encbeachmatBHBiobaseBiocGenericsBiocNeighborsBiocParallelBiocSingularblusterbootbroomcachemcarcarDatacirclizecliclueclustercodetoolscolorspacecommonmarkComplexHeatmapcorrplotcowplotcpp11crayoncurldata.tableDelayedArrayDerivdigestdoBydoParalleldplyrdqrngedgeRexactRankTestsfarverfastmapfastmatchfgseafitdistrplusforeachforecastformatRFormulafracdifffutile.loggerfutile.optionsgenericsGenomicRangesGetoptLongggforceggplot2ggpubrggraphggrepelggsciggsignifggtextGlobalOptionsgluegraphlayoutsgridExtragridtextgtableigraphIRangesirlbaisobanditeratorsjpegjsonlitelabelinglambda.rlatticelifecyclelimmalitedownlme4lmtestlocfitmagrittrmarkdownMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmaxstatmemoisemetapodmgcvminqamodelrmvtnormnlmenloptrnnetnumDerivpbkrtestpillarpkgconfigpngpolyclippolynompurrrquantregR6rbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasrjsonrlangrstatixrsvdS4ArraysS4VectorsS7ScaledMatrixscalesscranscuttleSeqinfoshapeSingleCellExperimentsitmosnowSparseArraySparseMstatmodstringistringrSummarizedExperimentsurvivalsurvminersystemfontstibbletidygraphtidyrtidyselecttimeDatetweenrurcautf8vctrsviridisviridisLitewithrxfunxml2XVectorzoo