Package: MOMA 1.19.0

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_1.19.0.tar.gz
MOMA_1.19.0.zip(r-4.5)MOMA_1.19.0.zip(r-4.4)MOMA_1.19.0.zip(r-4.3)
MOMA_1.19.0.tgz(r-4.4-any)MOMA_1.19.0.tgz(r-4.3-any)
MOMA_1.19.0.tar.gz(r-4.5-noble)MOMA_1.19.0.tar.gz(r-4.4-noble)
MOMA_1.19.0.tgz(r-4.4-emscripten)MOMA_1.19.0.tgz(r-4.3-emscripten)
MOMA.pdf |MOMA.html✨
MOMA/json (API)
NEWS

# 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-1.19.0(bioc 3.21)MOMA-1.18.0(bioc 3.20)

software networkenrichment networkinference network featureextraction clustering functionalgenomics transcriptomics systemsbiology

6.19 score 6 stars 13 scripts 141 downloads 128 mentions 5 exports 95 dependencies

Last updated 21 days agofrom:cd609f2d5c. Checks:OK: 1 WARNING: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 18 2024
R-4.5-win	WARNING	Nov 18 2024
R-4.5-linux	WARNING	Nov 18 2024
R-4.4-win	WARNING	Nov 18 2024
R-4.4-mac	WARNING	Nov 18 2024
R-4.3-win	WARNING	Nov 18 2024
R-4.3-mac	WARNING	Nov 18 2024

Exports:makeSaturationPlots mapEntrez mapHugo MomaConstructor sampleNameFilter

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

MOMA - Multi Omic Master Regulator Analysis

Sunny Jones, Evan Paull, Mariano Alvarez, Federico Giorgi and Andrea Califano

Rendered frommoma.Rmdusingknitr::rmarkdownon Nov 18 2024.

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