Package: MPAC 0.99.14

Peng Liu

MPAC: Multi-omic Pathway Analysis of Cancer

Multi-omic Pathway Analysis of Cancer (MPAC), integrates multi-omic data for understanding cancer 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]

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NEWS

# 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-0.99.13(bioc 3.20)

bioconductor-package

14 exports 1.38 score 103 dependencies

Last updated 22 days agofrom:b767726556

Exports:clSamp colPermIPL colRealIPL conMtf fltByPerm ovrGMT pltNeiStt ppCnInp ppPermInp ppRealInp ppRnaInp runPermPrd runPrd subNtw

Dependencies:abind askpass beachmat BH Biobase BiocGenerics BiocNeighbors BiocParallel BiocSingular bluster circlize cli clue cluster codetools colorspace ComplexHeatmap cowplot cpp11 crayon curl data.table DelayedArray DelayedMatrixStats digest doParallel dqrng edgeR fansi farver fastmatch fgsea fitdistrplus foreach formatR futile.logger futile.options GenomeInfoDb GenomeInfoDbData GenomicRanges GetoptLong ggplot2 GlobalOptions glue gtable httr igraph IRanges irlba isoband iterators jsonlite labeling lambda.r lattice lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats metapod mgcv mime munsell nlme openssl pillar pkgconfig png R6 RColorBrewer Rcpp RcppHNSW rjson rlang rsvd S4Arrays S4Vectors ScaledMatrix scales scran scuttle shape SingleCellExperiment sitmo snow SparseArray sparseMatrixStats statmod SummarizedExperiment survival sys tibble UCSC.utils utf8 vctrs viridisLite withr XVector zlibbioc

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Help page	Topics
Cluster samples by pathway over-representation	clSamp
Collect Inferred Pathway Levels (IPLs) from PARADIGM runs on permuted data	colPermIPL
Collect Inferred Pathway Levels (IPLs) from PARADIGM runs on real data	colRealIPL
Find consensus pathway motifs from a list of pathways	conMtf
Filter IPLs from real data by distribution from permuted data	fltByPerm
Calculate over-representation of gene sets in each sample by genes from sample's largest sub-pathway	ovrGMT
Plot a heatmap of pathway and omic states of a protein and its pathway neighbors	pltNeiStt
Prepare input copy-number (CN) alteration data to run PARADIGM	ppCnInp
Permute input genomic state data between genes in the same sample	ppPermInp
Prepare input copy-number (CN) alteration and RNA data to run PARADIGM	ppRealInp
Prepare input RNA data to run PARADIGM	ppRnaInp
Run PARADIGM on permuted data	runPermPrd
Run PARADIGM on multi-omic data	runPrd
Subset pathways by IPL results	subNtw

Package: MPAC 0.99.14

MPAC: Multi-omic Pathway Analysis of Cancer

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