Package: cosmosR 1.21.0

Aurélien Dugourd

cosmosR: COSMOS (Causal Oriented Search of Multi-Omic Space)

COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets based on prior knowledge of signaling, metabolic, and gene regulatory networks. It estimated the activities of transcrption factors and kinases and finds a network-level causal reasoning. Thereby, COSMOS provides mechanistic hypotheses for experimental observations across mulit-omics datasets.

Authors:Aurélien Dugourd [aut, cre], Attila Gabor [aut], Katharina Zirngibl [aut]

cosmosR_1.21.0.tar.gz
cosmosR_1.21.0.zip(r-4.7)cosmosR_1.21.0.zip(r-4.6)cosmosR_1.21.0.zip(r-4.5)
cosmosR_1.21.0.tgz(r-4.6-any)cosmosR_1.21.0.tgz(r-4.5-any)
cosmosR_1.21.0.tar.gz(r-4.7-any)cosmosR_1.21.0.tar.gz(r-4.6-any)
cosmosR_1.21.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
cosmosR/json (API)

# Install 'cosmosR' in R:

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

Bug tracker:https://github.com/saezlab/cosmosr/issues

Datasets:

HMDB_mapper_vec - Toy Input Transcription Data Set
meta_network - Meta Prior Knowledge Network
toy_metabolic_input - Toy Metabolic Input Data
toy_network - Toy Input Network
toy_RNA - Toy Input Transcription Data Set
toy_signaling_input - Toy Signaling Input

On BioConductor:cosmosR-1.19.1(bioc 3.23)cosmosR-1.18.1(bioc 3.22)

cellbiology pathways network proteomics metabolomics transcriptomics genesignaling data-integration metabolomic-data network-modelling phosphoproteomics

8.97 score 69 stars 1 packages 42 scripts 438 downloads 26 exports 96 dependencies

Last updated from:cfa5f2700a. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

The latest version of this package failed to build. Look at thebuild logs for more information.

Target	Result	Time
bioc-checks	WARNING	234
linux-devel-x86_64	NOTE	415
source / vignettes	OK	285
linux-release-x86_64	NOTE	310
macos-release-arm64	NOTE	166
macos-oldrel-arm64	NOTE	147
windows-devel	NOTE	384
windows-release	NOTE	169
windows-oldrel	NOTE	193
wasm-release	OK	186

Exports:compress_same_children createLinearColors decompress_moon_result decompress_solution_network decoupleRnival default_CARNIVAL_options display_node_neighboorhood extract_nodes_for_ORA filter_incohrent_TF_target format_COSMOS_res format_LR_ressource get_moon_scoring_network load_tf_regulon_dorothea make_heatmap_color_palette meta_network_cleanup moon prepare_metab_inputs preprocess_COSMOS_metabolism_to_signaling preprocess_COSMOS_signaling_to_metabolism reduce_solution_network reduce_solution_network_double_thresh run_COSMOS_metabolism_to_signaling run_COSMOS_signaling_to_metabolism translate_column_HMDB translate_res wide_ulm_res

Dependencies:annotate AnnotationDbi askpass backports base64enc bcellViper BH Biobase BiocGenerics BiocParallel Biostrings bit bit64 blob broom bslib cachem CARNIVAL cli clipr codetools cpp11 crayon curl DBI decoupleR digest dorothea dplyr evaluate fastmap fontawesome formatR fs futile.logger futile.options generics glue graph GSEABase highr hms htmltools htmlwidgets httr igraph IRanges jquerylib jsonlite KEGGREST knitr lambda.r lattice lifecycle lpSolve magrittr Matrix memoise mime openssl parallelly pillar pkgconfig png prettyunits progress purrr R6 rappdirs readr rjson rlang rmarkdown RSQLite S4Vectors sass Seqinfo snow stringi stringr sys tibble tidyr tidyselect tinytex tzdb utf8 vctrs visNetwork vroom withr xfun XML xtable XVector yaml

MOFA to COSMOS tutorial

Rendered fromMOFA_to_COSMOS.Rmdusingknitr::rmarkdown

Last update: 2026-03-12
Started: 2024-06-06

NCI60 tutorial

Rendered fromNCI60_tutorial.Rmdusingknitr::rmarkdown

Last update: 2024-06-06
Started: 2024-06-06

COSMOS-tutorial

Rendered fromtutorial.Rmdusingknitr::rmarkdown

Last update: 2023-03-27
Started: 2020-11-10

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Compress Network by Merging Nodes with Identical Children	compress_same_children
Create Cosmos Data	cosmos_data
Create Linear Colors Based on Numeric Input	createLinearColors
Decompress Moon Result	decompress_moon_result
Decompress Solution Network	decompress_solution_network
DecoupleRnival	decoupleRnival
Setting Default CARNIVAL Options	default_CARNIVAL_options
display_node_neighboorhood	display_node_neighboorhood
Extract COSMOS nodes for ORA analysis	extract_nodes_for_ORA
filter_incohrent_TF_target	filter_incohrent_TF_target
format_COSMOS_res	format_COSMOS_res
Format Ligand-Receptor Resource	format_LR_ressource
Get Moon Scoring Network	get_moon_scoring_network
Convert gmt file to data frame	gmt_to_dataframe
Toy Input Transcription Data Set	HMDB_mapper_vec
load transcription factor regulon	load_tf_regulon_dorothea
Create Heatmap Color Palette	make_heatmap_color_palette
Meta Prior Knowledge Network	meta_network
meta_network_cleanup	meta_network_cleanup
moon	moon
add metabolic compartment and metab__ prefix to metabolite IDs	prepare_metab_inputs
Preprocess COSMOS Inputs For Metabolism to Signaling	preprocess_COSMOS_metabolism_to_signaling
Preprocess COSMOS Inputs For Signaling to Metabolism	preprocess_COSMOS_signaling_to_metabolism
Print Cosmos Data Summary Print a summary of cosmos data.	print.cosmos_data
reduce_solution_network	reduce_solution_network
reduce_solution_network_double_thresh	reduce_solution_network_double_thresh
run COSMOS metabolism to signaling	run_COSMOS_metabolism_to_signaling
run COSMOS signaling to metabolism	run_COSMOS_signaling_to_metabolism
Toy Metabolic Input Data	toy_metabolic_input
Toy Input Network	toy_network
Toy Input Transcription Data Set	toy_RNA
Toy Signaling Input	toy_signaling_input
Translate Column Using HMDB Mapper	translate_column_HMDB
translate_res	translate_res
Convert ULM Results to Wide Format	wide_ulm_res