Package: MPAC 1.6.0

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_1.6.0.tar.gz
MPAC_1.6.0.zip(r-4.7)MPAC_1.6.0.zip(r-4.6)MPAC_1.6.0.zip(r-4.5)
MPAC_1.6.0.tgz(r-4.6-any)MPAC_1.6.0.tgz(r-4.5-any)
MPAC_1.6.0.tar.gz(r-4.7-any)MPAC_1.6.0.tar.gz(r-4.6-any)
MPAC_1.6.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
MPAC/json (API)
NEWS

# Install 'MPAC' in R:
install.packages('MPAC', repos = c('https://bioc-release.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

3.48 score 4 scripts 244 downloads 20 exports 161 dependencies

Last updated from:2a03ee8ae4 (on RELEASE_3_23). Checks:8 WARNING, 1 ERROR, 1 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksWARNING237
linux-devel-x86_64WARNING428
source / vignettesERROR309
linux-release-x86_64WARNING347
macos-release-arm64WARNING285
macos-oldrel-arm64WARNING195
windows-develWARNING548
windows-releaseWARNING304
windows-oldrelWARNING581
wasm-releaseOK165

Exports:clSampcolPermIPLcolRealIPLconMtffltByPermgetSignifOvrOnClovrGMTpltConMtfpltMtfPrtIPLpltNeiSttpltOvrHmpltSttKMppCnInpppPermInpppRealInpppRnaInpppRunPrdrunPermPrdrunPrdsubNtw

Dependencies:abindassortheadbackportsbase64encbeachmatBHBiobaseBiocGenericsBiocNeighborsBiocParallelBiocSingularblusterbootbroomcachemcarcarDatacirclizecliclueclustercodetoolscolorspacecommonmarkComplexHeatmapcorrplotcowplotcpp11crayoncurldata.tableDelayedArrayDerivdigestdoBydoParalleldplyrdqrngedgeRexactRankTestsfarverfastmapfastmatchfgseafitdistrplusforeachforecastformatRFormulafracdifffutile.loggerfutile.optionsgenericsGenomicRangesGetoptLongggforceggplot2ggpubrggraphggrepelggsciggsignifggtextGlobalOptionsgluegraphlayoutsgridExtragridtextgtableigraphIRangesirlbaisobanditeratorsjpegjsonlitelabelinglambda.rlatticelifecyclelimmalitedownlme4lmtestlocfitmagrittrmarkdownMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmaxstatmemoisemetapodmgcvmicrobenchmarkminqamodelrmvtnormnlmenloptrnnetnumDerivpbkrtestpillarpkgconfigpngpolyclippolynompurrrquantregR6rbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasrjsonrlangrstatixrsvdS4ArraysS4VectorsS7ScaledMatrixscalesscranscuttleSeqinfoshapeSingleCellExperimentsitmosnowSparseArraySparseMstatmodstringistringrSummarizedExperimentsurvivalsurvminersystemfontstibbletidygraphtidyrtidyselecttimeDatetweenrurcautf8vctrsviridisviridisLitewithrxfunxml2XVectorzoo