Package: cosmosR 1.13.0
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:
cosmosR_1.13.0.tar.gz
cosmosR_1.13.0.zip(r-4.5)cosmosR_1.13.0.zip(r-4.4)cosmosR_1.13.0.zip(r-4.3)
cosmosR_1.13.0.tgz(r-4.4-any)cosmosR_1.13.0.tgz(r-4.3-any)
cosmosR_1.13.0.tar.gz(r-4.5-noble)cosmosR_1.13.0.tar.gz(r-4.4-noble)
cosmosR_1.13.0.tgz(r-4.4-emscripten)cosmosR_1.13.0.tgz(r-4.3-emscripten)
cosmosR.pdf |cosmosR.html✨
cosmosR/json (API)
NEWS
# 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
- HMDB_mapper_vec - Toy Input Transcription Data Set
- meta_network - Meta Prior Knowledge Network
- toy_RNA - Toy Input Transcription Data Set
- toy_metabolic_input - Toy Metabolic Input Data
- toy_network - Toy Input Network
- toy_signaling_input - Toy Signaling Input
On BioConductor:cosmosR-1.13.0(bioc 3.20)cosmosR-1.12.0(bioc 3.19)
Last updated 2 months agofrom:4c05998b1b
Exports:compress_same_childrendecompress_solution_networkdecoupleRnivaldefault_CARNIVAL_optionsdisplay_node_neighboorhoodextract_nodes_for_ORAfilter_incohrent_TF_targetformat_COSMOS_resload_tf_regulon_dorotheameta_network_cleanupprepare_metab_inputspreprocess_COSMOS_metabolism_to_signalingpreprocess_COSMOS_signaling_to_metabolismreduce_solution_networkrun_COSMOS_metabolism_to_signalingrun_COSMOS_signaling_to_metabolism
Dependencies:annotateAnnotationDbiaskpassbackportsbase64encbcellViperBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64blobbroombslibcachemCARNIVALclicliprcodetoolscpp11crayoncurlDBIdecoupleRdigestdorotheadplyrevaluatefansifastmapfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDatagluegraphGSEABasehighrhmshtmltoolshtmlwidgetshttrigraphIRangesjquerylibjsonliteKEGGRESTknitrlambda.rlatticelifecyclelpSolvemagrittrMatrixmemoisemimeopensslparallellypillarpkgconfigplogrpngprettyunitsprogresspurrrR6rappdirsreadrrjsonrlangrmarkdownRSQLiteS4VectorssasssnowstringistringrsystibbletidyrtidyselecttinytextzdbUCSC.utilsutf8vctrsvisNetworkvroomwithrxfunXMLxtableXVectoryamlzlibbioc