Package: MOMA 1.25.0

Sunny Jones

MOMA: Multi Omic Master Regulator Analysis

This package implements the inference of candidate master regulator proteins from multi-omics' data (MOMA) algorithm, as well as ancillary analysis and visualization functions.

Authors:Evan Paull [aut], Sunny Jones [aut, cre], Mariano Alvarez [aut]

MOMA_1.25.0.tar.gz
MOMA_1.25.0.zip(r-4.7)MOMA_1.25.0.zip(r-4.6)MOMA_1.25.0.zip(r-4.5)
MOMA_1.25.0.tgz(r-4.6-any)MOMA_1.25.0.tgz(r-4.5-any)
MOMA_1.25.0.tar.gz(r-4.7-any)MOMA_1.25.0.tar.gz(r-4.6-any)
MOMA_1.25.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
MOMA/json (API)

# Install 'MOMA' in R:

install.packages('MOMA', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/califano-lab/moma/issues

Datasets:

example.gbm.mae - Glioblastoma (GBM) Example Dataset
gbm.pathways - Glioblastoma (GBM) Pathways
gene.map - Gene Location Mapping
mutSig - MutSig Blacklisted genes

On BioConductor:MOMA-1.25.0(bioc 3.24)MOMA-1.24.0(bioc 3.23)

software networkenrichment networkinference network featureextraction clustering functionalgenomics transcriptomics systemsbiology

6.23 score 6 stars 14 scripts 369 downloads 128 mentions 5 exports 81 dependencies

Last updated from:e936c02636. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	209
linux-devel-x86_64	OK	440
source / vignettes	OK	321
linux-release-x86_64	OK	396
macos-release-arm64	OK	210
macos-oldrel-arm64	OK	174
windows-devel	OK	261
windows-release	OK	245
windows-oldrel	OK	243
wasm-release	OK	187

Exports:makeSaturationPlots mapEntrez mapHugo MomaConstructor sampleNameFilter

Dependencies:abind Biobase BiocBaseUtils BiocGenerics bit bit64 circlize cli clipr clue cluster codetools colorspace ComplexHeatmap cpp11 crayon DelayedArray DEoptimR digest doParallel dplyr farver foreach generics GenomicRanges GetoptLong ggplot2 GlobalOptions glue gtable hms IRanges isoband iterators labeling lattice lifecycle limma magrittr Matrix MatrixGenerics matrixStats MKmisc MultiAssayExperiment pillar pkgconfig plyr png prettyunits progress purrr qvalue R6 RColorBrewer Rcpp readr reshape2 rjson rlang robustbase S4Arrays S4Vectors S7 scales Seqinfo shape SparseArray statmod stringi stringr SummarizedExperiment tibble tidyr tidyselect tzdb utf8 vctrs viridisLite vroom withr XVector

MOMA - Multi Omic Master Regulator Analysis

Rendered frommoma.Rmdusingknitr::rmarkdown

Last update: 2020-04-29
Started: 2020-04-02

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Integrate CNV scores	cnvScoreStouffer
Glioblastoma (GBM) Example Dataset	example.gbm.mae
Glioblastoma (GBM) Pathways	gbm.pathways
Gene Location Mapping	gene.map
Main function to generate the summary plots of the analysis	makeSaturationPlots
Convert from entrez ids to hugo gene names	mapEntrez
Convert from hugo gene names to entrez ids	mapHugo
Map scores to cytoband location	mapScoresCnvBand
MOMA Object	Moma Moma-class
MOMA Constructor Function	MomaConstructor
MutSig Blacklisted genes	mutSig
Retain TCGA sample ids without the final letter designation ('A/B/C')	sampleNameFilter
dispatch method for either CNV location corrected or SNV	stoufferIntegrate
Use Stouffer's method to combine z-scores of DIGGIT interactions for each cMR protein.	stoufferIntegrateDiggit