Package: SUMO 1.2.3

Bernard Isekah Osangir

SUMO: Generating Multi-Omics Datasets for Testing and Benchmarking

Provides tools to simulate multi-omics datasets with predefined signal structures. The generated data can be used for testing, validating, and benchmarking integrative analysis methods such as factor models and clustering approaches. This version includes enhanced signal customization, visualization tools (scatter, histogram, 3D), MOFA-based analysis pipelines, PowerPoint export, and statistical profiling of datasets. Designed for both method development and teaching, SUMO supports real and synthetic data pipelines with interpretable outputs. Tini, Giulia, et al (2019) <doi:10.1093/bib/bbx167>.

Authors:Bernard Isekah Osang'ir [aut, cre], Ziv Shkedy [ctb], Surya Gupta [ctb], Jürgen Claesen [ctb]

SUMO_1.2.3.tar.gz
SUMO_1.2.3.tar.gz(r-4.7-any)SUMO_1.2.3.tar.gz(r-4.6-any)
SUMO_1.2.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
SUMO/json (API)
NEWS

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

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

1.48 score 8 scripts 201 downloads 18 exports 102 dependencies

Last updated from:c655ec4bbe. Checks:2 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64NOTE232
source / vignettesOK235
linux-release-x86_64NOTE222
wasm-releaseOK172

Exports:as_multiomicscompute_means_varsdemo_multiomics_analysisdivide_features_onedivide_features_twodivide_samplesdivide_vectorfeature_selection_onefeature_selection_twoplot_factorplot_simDataplot_weightssimulate_twoOmicsDatasimulateMultiOmicssumo_load_pretrained_mofasumo_pretrained_mofa_availablesumo_pretrained_mofa_pathsumo_setup_mofa

Dependencies:askpassbackportsbase64encbitbit64blobbroombslibcachemcallrcellrangerclicliprconflictedcpp11crayoncurldata.tableDBIdbplyrdigestdplyrdtplyrevaluatefarverfastmapfontawesomeforcatsfsgarglegenericsggplot2gluegoogledrivegooglesheets4gridExtragtablehavenhighrhmshtmltoolshttridsisobandjquerylibjsonliteknitrlabelinglifecyclelubridatemagrittrmemoisemimemodelrofficeropensslpillarpkgconfigprettyunitsprocessxprogresspspurrrR6raggrappdirsRColorBrewerreadrreadxlrematchrematch2reprexrlangrmarkdownrstudioapirvestS7sassscalesselectrstringistringrsyssystemfontstextshapingtibbletidyrtidyselecttidyversetimechangetinytextzdbutf8uuidvctrsviridisLitevroomwithrxfunxml2yamlzip

Readme and manuals

Help Manual

Help pageTopics
Convert legacy objects (e.g., from 'simulate_twoOmicsData()') to the current standardized structure used by downstream tools.as_multiomics
Compute Summary Statistics for a List of Datasetscompute_means_vars
Demonstration of SUMO Utility in Multi-Omics Analysis using MOFA2demo_multiomics_analysis
Dividing features to create vectors with signal in the first omic for single datadivide_features_one
Dividing features to create vectors with signal in the second omic for single datadivide_features_two
Global Variabledivide_samples
#' Global Variable #' #' A global variable used in multiple functions. #' #'divide_vector
Dividing features to create vectors with signal in the first omicfeature_selection_one
Dividing features to create vectors with signal in the second omicfeature_selection_two
Visualization of factor scores (ground truth)plot_factor
Visualize simulated multi-omics data as a heatmapplot_simData
Visualize feature loadings (weights)plot_weights
Simulation of omics with predefined single or multiple latent factors in multi-omicssimulate_twoOmicsData
Simulation of omics with predefined single or multiple latent factors in multi-omicssimulateMultiOmics
SUMO: Simulation Utilities for Multi-Omics DataSUMO-package SUMO
Load a pretrained MOFA model (no Python required)sumo_load_pretrained_mofa
List pretrained MOFA models included with SUMOsumo_pretrained_mofa_available
Path to a pretrained MOFA model shipped with SUMOsumo_pretrained_mofa_path
Interactive setup for Python 'mofapy2' via reticulate (fallback when basilisk is unavailable)sumo_setup_mofa