{ "_id": "6ae770682e87f76f20acd343", "Package": "MOSim", "Title": "Multi-Omics Simulation (MOSim)", "Version": "2.9.0", "Authors@R": "c(person(\"Carolina\", \"Monzó\", email = \"carolmonzoc@gmail.com\", role = c(\"aut\")), person(\"Carlos\", \"Martínez\", email = \"cmarmir@gmail.com\", role = \"aut\"), person(\"Sonia\", \"Tarazona\", email = \"sotacam@gmail.com\", role = c(\"cre\", \"aut\")))", "Description": "MOSim package simulates multi-omic experiments that mimic\nregulatory mechanisms within the cell, allowing flexible\nexperimental design including time course and multiple groups.", "Encoding": "UTF-8", "License": "GPL-3", "LazyData": "false", "biocViews": "Software, TimeCourse, ExperimentalDesign, RNASeq", "BugReports": "https://github.com/ConesaLab/MOSim/issues", "URL": "https://github.com/ConesaLab/MOSim", "Collate": "'AllClass.R' 'AllGeneric.R' 'Simulator.R' 'SimulatorRegion.R'\n'ChIP-seq.R' 'DNase-seq.R' 'MOSim-package.R' 'functions.R'\n'Simulation.R' 'MOSim.R' 'RNA-seq.R' 'data.R'\n'simulate_WGBS_functions.R' 'methyl-seq.R' 'miRNA-seq.R'\n'sc_MOSim.R' 'sc_coexpression.R' 'sparsim_functions.R' 'zzz.R'", "RoxygenNote": "7.3.2", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "cmake libglpk-dev make libbz2-dev libicu-dev\nliblzma-dev libpng-dev libuv1-dev libxml2-dev libssl-dev\npython3 xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:50:46 UTC", "RemoteUrl": "https://github.com/bioc/MOSim", "RemoteRef": "HEAD", "RemoteSha": "76f9819e904131dc41b557a19b25a5921dfcdd7a", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-11-01 14:06:20 UTC", "User": "root" }, "Author": "Carolina Monzó [aut],\nCarlos Martínez [aut],\nSonia Tarazona [cre, aut]", "Maintainer": "Sonia Tarazona ", "_user": "bioc", "_type": "src", "_file": "MOSim_2.9.0.tar.gz", "_fileid": "https://r2.ropensci.org/6398ed3f19fa701162e389116af5b62ce4ce79d665715b8b59c364f2357c4075", "_filesize": 6441678, "_sha256": "6398ed3f19fa701162e389116af5b62ce4ce79d665715b8b59c364f2357c4075", "_expires": "2027-02-09T17:01:25.000Z", "_created": "2026-11-01T14:06:20.000Z", "_published": "2026-11-01T17:01:28.385Z", "_upstream": "https://github.com/bioc/MOSim", "_status": "success", "_maintainer": { "name": "Sonia Tarazona", "email": "sotacam@gmail.com", "login": "soniatarazona", "description": "", "uuid": 63703888 }, "_jobs": [ { "job": 124871916427, "time": 257, "config": "bioc-checks", "r": "4.6.2", "check": "ERROR", "artifact": "13086874670" }, { "job": 124871916498, "time": 625, "config": "linux-devel-arm64", "r": "4.7.0", "check": "WARNING", "artifact": "13086917433" }, { "job": 124871916425, "time": 629, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "13087483922" }, { "job": 124871916414, "time": 564, "config": "linux-release-arm64", "r": "4.6.2", "check": "WARNING", "artifact": "13086718117" }, { "job": 124871916440, "time": 623, "config": "linux-release-x86_64", "r": "4.6.2", "check": "WARNING", "artifact": "13087434257" }, { "job": 124871916433, "time": 385, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "13092138949" }, { "job": 124871916513, "time": 1204, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "13091729268" }, { "job": 124871916437, "time": 639, "config": "macos-release-arm64", "r": "4.6.2", "check": "WARNING", "artifact": "13092815871" }, { "job": 124871916430, "time": 1291, "config": "macos-release-x86_64", "r": "4.6.2", "check": "WARNING", "artifact": "13092337067" }, { "job": 124862126325, "time": 586, "config": "source", "r": "4.6.2", "check": "OK", "artifact": "13086354963" }, { "job": 124871916422, "time": 171, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "13087331972" }, { "job": 124871916488, "time": 834, "config": "windows-devel-arm64", "r": "4.7.0", "check": "WARNING", "artifact": "13087137489" }, { "job": 124871916464, "time": 782, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "13087001529" }, { "job": 124871916512, "time": 578, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "13086892280" }, { "job": 124871916511, "time": 801, "config": "windows-release-arm64", "r": "4.6.2", "check": "WARNING", "artifact": "13087675439" }, { "job": 124871916442, "time": 737, "config": "windows-release-x86_64", "r": "4.6.2", "check": "WARNING", "artifact": "13087520594" } ], "_bioccheck": { "error": 1, "warning": 4, "note": 13 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/41310238613", "_commit": { "id": "76f9819e904131dc41b557a19b25a5921dfcdd7a", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380646 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.2.0", "role": "Depends" }, { "package": "cpp11", "role": "LinkingTo" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "HiddenMarkov", "role": "Imports" }, { "package": "zoo", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "lazyeval", "role": "Imports" }, { "package": "matrixStats", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "stringi", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "scran", "role": "Imports" }, { "package": "Seurat", "role": "Imports" }, { "package": "Signac", "role": "Imports" }, { "package": "edgeR", "role": "Imports" }, { "package": "Rcpp", "role": "Imports" }, { "package": "testthat", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "codetools", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "stats", "role": "Suggests" }, { "package": "utils", "role": "Suggests" }, { "package": "purrr", "role": "Suggests" }, { "package": "scales", "role": "Suggests" }, { "package": "tibble", "role": "Suggests" }, { "package": "tidyr", "role": "Suggests" }, { "package": "Biobase", "role": "Suggests" }, { "package": "scater", "role": "Suggests" }, { "package": "SingleCellExperiment", "role": "Suggests" }, { "package": "decor", "role": "Suggests" }, { "package": "markdown", "role": "Suggests" }, { "package": "Rsamtools", "role": "Suggests" }, { "package": "igraph", "role": "Suggests" }, { "package": "leiden", "role": "Suggests" }, { "package": "bluster", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-07", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "2.9.0", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "2.8.0", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "software", "timecourse", "experimentaldesign", "rnaseq", "cpp" ], "_stars": 14, "_contributors": [ { "user": "carolinamonzo", "count": 124, "uuid": 24670602 }, { "user": "ariannafebbo", "count": 14, "uuid": 18719368 }, { "user": "nturaga", "count": 12, "uuid": 2746443 }, { "user": "jwokaty", "count": 6, "uuid": 1744257 }, { "user": "neurergus", "count": 6, "uuid": 195449 }, { "user": "soniatarazona", "count": 3, "uuid": 63703888 }, { "user": "aarzalluz", "count": 1, "uuid": 19856199 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 482, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 662, "source": "https://www.bioconductor.org/packages/stats/bioc/MOSim" }, "_mentions": 4, "_devurl": "https://github.com/conesalab/mosim", "_searchresults": 12, "_abi": { "exports": [ { "key": "MOSim::MOSimulation", "hash": "624e62b6a19ae785" }, { "key": "MOSim::MOSimulator", "hash": "295fb672d6cc3278" }, { "key": "MOSim::MOSimulatorRegion", "hash": "946418b8bb90cf85" }, { "key": "MOSim::SimChIPseq", "hash": "6a07c8dd0365b852" }, { "key": "MOSim::SimDNaseseq", "hash": "52539d5521851bcb" }, { "key": "MOSim::SimMethylseq", "hash": "fede698a6dee16ce" }, { "key": "MOSim::SimRNAseq", "hash": "bff70bd55edbd5c7" }, { "key": "MOSim::SimTF", "hash": "ab6d74a05305b19b" }, { "key": "MOSim::SimmiRNAseq", "hash": "0845739c975bc3af" }, { "key": "MOSim::generic:IDfromGenes", "hash": "e4af710ef9b53c2e" }, { "key": "MOSim::generic:IDtoGenes", "hash": "ddbe19ceffc979aa" }, { "key": "MOSim::generic:adjustProfiles", "hash": "077b446c28b8c600" }, { "key": "MOSim::generic:initializeData", "hash": "12ad119c03069bbb" }, { "key": "MOSim::generic:locGRanges", "hash": "6323bf7611e6dae9" }, { "key": "MOSim::generic:postSimulation", "hash": "43c9a1d83208fb54" }, { "key": "MOSim::generic:regionNames", "hash": "c534430902922a1c" }, { "key": "MOSim::generic:simSettings", "hash": "f1de95ba51085aed" }, { "key": "MOSim::generic:simulate", "hash": "f391532808d958f9" }, { "key": "MOSim::generic:simulateParams", "hash": "65b87da4ec1e004e" } ], "imports": [ { "key": "Rcpp::Rcpp_precious_preserve()", "hash": "33a97ea62b293da6" }, { "key": "Rcpp::Rcpp_precious_remove()", "hash": "63d26947ba7e1377" }, { "key": "Rcpp::dataptr()", "hash": "54e69ad2e6668c83" }, { "key": "Rcpp::demangle()", "hash": "b0cfd6754c5ebc4e" }, { "key": "Rcpp::enterRNGScope()", "hash": "a04a299137cef947" }, { "key": "Rcpp::exitRNGScope()", "hash": "a04a299137cef947" }, { "key": "Rcpp::rcpp_get_stack_trace()", "hash": "c684a9bbe15cdc52" }, { "key": "Rcpp::rcpp_set_stack_trace()", "hash": "33a97ea62b293da6" } ] }, "_rbuild": "4.6.2", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/MOSim.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md" ], "_homeurl": "https://github.com/conesalab/mosim", "_realowner": "bioc", "_cranurl": false, "_exports": [ "calculate_mean_per_list_df", "check_patterns", "discretize", "experimentalDesign", "make_association_dataframe", "make_cluster_patterns", "match_gene_regulator", "match_gene_regulator_cluster", "mosim", "omicData", "omicResults", "omicSettings", "omicSim", "plotProfile", "random_unif_interval", "sc_mosim", "sc_omicData", "sc_omicResults", "sc_omicSettings", "sc_param_estimation", "shuffle_group_matrix", "simulate_coexpression", "sparsim_create_simulation_parameter", "sparsim_estimate_intensity", "sparsim_estimate_library_size", "sparsim_estimate_parameter_from_data", "sparsim_estimate_variability", "sparsim_simulation" ], "_datasets": [ { "name": "associationList", "title": "Data to showcase scRNA and scATAC-seq association", "object": "associationList", "file": "associationList.rda", "class": [ "data.frame" ], "fields": [ "Peak_ID", "Gene_ID" ], "rows": 10000, "table": true, "tojson": true }, { "name": "sampleData", "title": "Default data", "object": "sampleData", "file": "sampleData.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "scatac", "title": "Data to test scMOSim", "object": "scatac", "file": "scatac.rda", "class": [ "matrix", "array" ], "fields": [ "AAACATGCAGCAAGTG-1", "AAAGGCTCACAGCCAT-1", "AACCGCTCATCTAGCA-1", "AAGCTAGAGTTCCTGC-1", "AAGCTATGTGCTGGTG-1", "AAGCTCCCAGATAGAC-1", "AAGGTCAAGCCTAACG-1", "AAGGTCAAGGAAGTAT-1", "AAGTTTGTCACATTGA-1", "AATTTGCCAATACTGT-1", "AAACCGGCATAATCAC-1", "AAAGCACCATTGTGGC-1", "AACCGCTCAGCTTACA-1", "AACCTTAAGCGGCTGT-1", "AACTAGTGTGGACCTG-1", "AAGCTATGTTTAACGG-1", "AAGTAGCCAGGAACCA-1", "AAGTGAAGTCACCAAA-1", "AATAGAGGTGCTCACC-1", "AATCTCAAGAAACTGG-1", "AAAGCGGGTTGCACAA-1", "AACATCATCAGTGAAG-1", "AACTACTCATAATCGT-1", "AAGAATCAGCTATATG-1", "AAGAATCAGGAGGGTT-1", "AAGCAAGTCACGCCAA-1", "AAGCAAGTCCCTCACG-1", "AAGCCTGTCTAGCGAT-1", "AAGCTAGAGGCACAGG-1", "AAGCTATGTATTACCC-1", "AAAGGTTAGGCGAAAC-1", "AACAAAGGTGTCCTGC-1", "AACAGCAAGCGCAATT-1", "AACATCATCAGCATTA-1", "AACCGGCTCAGGCCTA-1", "AACCTCCTCTCATCAT-1", "AACCTTGCAGTTTGTG-1", "AACTAGTGTTACGCAA-1", "AACTGTTCATCCCTCA-1", "AAGAATCAGAGCCGGA-1" ], "rows": 108377, "table": true, "tojson": true }, { "name": "scrna", "title": "Data to test scMOSim", "object": "scrna", "file": "scrna.rda", "class": [ "matrix", "array" ], "fields": [ "AAACATGCAGCAAGTG-1", "AAAGGCTCACAGCCAT-1", "AACCGCTCATCTAGCA-1", "AAGCTAGAGTTCCTGC-1", "AAGCTATGTGCTGGTG-1", "AAGCTCCCAGATAGAC-1", "AAGGTCAAGCCTAACG-1", "AAGGTCAAGGAAGTAT-1", "AAGTTTGTCACATTGA-1", "AATTTGCCAATACTGT-1", "AAACCGGCATAATCAC-1", "AAAGCACCATTGTGGC-1", "AACCGCTCAGCTTACA-1", "AACCTTAAGCGGCTGT-1", "AACTAGTGTGGACCTG-1", "AAGCTATGTTTAACGG-1", "AAGTAGCCAGGAACCA-1", "AAGTGAAGTCACCAAA-1", "AATAGAGGTGCTCACC-1", "AATCTCAAGAAACTGG-1", "AAAGCGGGTTGCACAA-1", "AACATCATCAGTGAAG-1", "AACTACTCATAATCGT-1", "AAGAATCAGCTATATG-1", "AAGAATCAGGAGGGTT-1", "AAGCAAGTCACGCCAA-1", "AAGCAAGTCCCTCACG-1", "AAGCCTGTCTAGCGAT-1", "AAGCTAGAGGCACAGG-1", "AAGCTATGTATTACCC-1", "AAAGGTTAGGCGAAAC-1", "AACAAAGGTGTCCTGC-1", "AACAGCAAGCGCAATT-1", "AACATCATCAGCATTA-1", "AACCGGCTCAGGCCTA-1", "AACCTCCTCTCATCAT-1", "AACCTTGCAGTTTGTG-1", "AACTAGTGTTACGCAA-1", "AACTGTTCATCCCTCA-1", "AAGAATCAGAGCCGGA-1" ], "rows": 36601, "table": true, "tojson": true }, { "name": "TF_human", "title": "Data to extract human TF", "object": "TF_human", "file": "TF_human.rda", "class": [ "data.frame" ], "fields": [ "TF", "Target_gene" ], "rows": 16634, "table": true, "tojson": true } ], "_help": [ { "page": "associationList", "title": "Data to showcase scRNA and scATAC-seq association", "topics": [ "associationList" ] }, { "page": "calculate_mean_per_list_df", "title": "calculate_mean_per_list_df", "topics": [ "calculate_mean_per_list_df" ] }, { "page": "check_patterns", "title": "check_patterns", "topics": [ "check_patterns" ] }, { "page": "discretize", "title": "Discretize ChIP-Seq counts to simulate a binary dataset", "topics": [ "discretize" ] }, { "page": "experimentalDesign", "title": "Retrieves the experimental design", "topics": [ "experimentalDesign" ] }, { "page": "is.declared", "title": "Check if a variable is declared.", "topics": [ "is.declared" ] }, { "page": "make_association_dataframe", "title": "make_association_dataframe", "topics": [ "make_association_dataframe" ] }, { "page": "make_cluster_patterns", "title": "make_cluster_patterns", "topics": [ "make_cluster_patterns" ] }, { "page": "match_gene_regulator", "title": "match_gene_regulator", "topics": [ "match_gene_regulator" ] }, { "page": "match_gene_regulator_cluster", "title": "match_gene_regulator_cluster", "topics": [ "match_gene_regulator_cluster" ] }, { "page": "mosim", "title": "mosim", "topics": [ "mosim" ] }, { "page": "omicData", "title": "Set customized data for an omic.", "topics": [ "omicData" ] }, { "page": "omicResults", "title": "Retrieves the simulated data.", "topics": [ "omicResults" ] }, { "page": "omicSettings", "title": "Retrieves the settings used in a simulation", "topics": [ "omicSettings" ] }, { "page": "omicSim", "title": "Set the simulation settings for an omic.", "topics": [ "omicSim" ] }, { "page": "plotProfile", "title": "Generate a plot of a feature's profile for one or two omics.", "topics": [ "plotProfile" ] }, { "page": "random_unif_interval", "title": "random_unif_interval Function to call the C code This function is a copy of the `random_unif_interval` function from the `SPARSim` package (v0.9.5), originally developed by Giacomo Baruzzo, Ilaria Patuzzi, Barbara Di Camillo (2020). The original package is licensed under the GPL-3 license.", "topics": [ "random_unif_interval" ] }, { "page": "sampleData", "title": "Default data", "topics": [ "sampleData" ] }, { "page": "sc_mosim", "title": "sc_mosim", "topics": [ "sc_mosim" ] }, { "page": "sc_omicData", "title": "sc_omicData", "topics": [ "sc_omicData" ] }, { "page": "sc_omicResults", "title": "sc_omicResults", "topics": [ "sc_omicResults" ] }, { "page": "sc_omicSettings", "title": "sc_omicSettings", "topics": [ "sc_omicSettings" ] }, { "page": "sc_param_estimation", "title": "sc_param_estimation", "topics": [ "sc_param_estimation" ] }, { "page": "scatac", "title": "Data to test scMOSim", "topics": [ "scatac" ] }, { "page": "scrna", "title": "Data to test scMOSim", "topics": [ "scrna" ] }, { "page": "shuffle_group_matrix", "title": "shuffle_group_matrix, Reorder cell type-specific expression matrix during co-expression simulation. Copied from ACORDE (https://github.com/ConesaLab/acorde) to facilitate stability and running within our scripts This function is a slightly modified copy of the `shuffle_group_matrix` function from the `Acorde` package (v1.0.0), originally developed by Arzalluz-Luque A, Salguero P, Tarazona S, Conesa A. (2022). acorde unravels functionally interpretable networks of isoform co-usage from single cell data. Nature communications 1828. DOI: 10.1038/s41467-022-29497-w. The original package is licensed under the GPL-3 license.", "topics": [ "shuffle_group_matrix" ] }, { "page": "simulate_coexpression", "title": "simulate coexpression", "topics": [ "simulate_coexpression" ] }, { "page": "simulate_hyper", "title": "Simulate technical variability", "topics": [ "simulate_hyper" ] }, { "page": "sparsim_create_simulation_parameter", "title": "Create SPARSim simulation parameter", "topics": [ "sparsim_create_simulation_parameter" ] }, { "page": "sparsim_estimate_intensity", "title": "Estimate SPARSIm \"intensity\" parameter", "topics": [ "sparsim_estimate_intensity" ] }, { "page": "sparsim_estimate_library_size", "title": "Estimate SPARSim \"library size\" parameter", "topics": [ "sparsim_estimate_library_size" ] }, { "page": "sparsim_estimate_parameter_from_data", "title": "Estimate SPARSim simulation parameter from a given count table", "topics": [ "sparsim_estimate_parameter_from_data" ] }, { "page": "sparsim_estimate_variability", "title": "Estimate SPARSim \"variability\" parameter", "topics": [ "sparsim_estimate_variability" ] }, { "page": "sparsim_simulation", "title": "Function to simulate a raw count table", "topics": [ "sparsim_simulation" ] }, { "page": "TF_human", "title": "Data to extract human TF", "topics": [ "TF_human" ] } ], "_readme": "https://github.com/bioc/MOSim/raw/HEAD/README.md", "_rundeps": [ "abind", "askpass", "assorthead", "base64enc", "beachmat", "BH", "Biobase", "BiocGenerics", "BiocNeighbors", "BiocParallel", "BiocSingular", "Biostrings", "bitops", "bluster", "bslib", "cachem", "caTools", "cli", "cluster", "codetools", "commonmark", "cowplot", "cpp11", "crayon", "crosstalk", "curl", "data.table", "DelayedArray", "deldir", "digest", "dotCall64", "dplyr", "dqrng", "edgeR", "evaluate", "farver", "fastDummies", "fastmap", "fastmatch", "fitdistrplus", "FNN", "fontawesome", "formatR", "fs", "futile.logger", "futile.options", "future", "future.apply", "generics", "GenomeInfoDb", "GenomicRanges", "ggplot2", "ggrepel", "ggridges", "globals", "glue", "goftest", "gplots", "gridExtra", "gtable", "gtools", "here", "HiddenMarkov", "highr", "htmltools", "htmlwidgets", "httpuv", "httr", "ica", "igraph", "IRanges", "irlba", "isoband", "jquerylib", "jsonlite", "KernSmooth", "knitr", "labeling", "lambda.r", "later", "lattice", "lazyeval", "lifecycle", "limma", "listenv", "lmtest", "magrittr", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "metapod", "mime", "miniUI", "nlme", "openssl", "otel", "parallelly", "patchwork", "pbapply", "pillar", "pkgconfig", "plotly", "plyr", "png", "polyclip", "progressr", "promises", "purrr", "R6", "RANN", "rappdirs", "RColorBrewer", "Rcpp", "RcppAnnoy", "RcppArmadillo", "RcppEigen", "RcppHNSW", "RcppProgress", "RcppRoll", "RcppThread", "RcppTOML", "reshape2", "reticulate", "Rhtslib", "rlang", "rmarkdown", "ROCR", "rprojroot", "Rsamtools", "RSpectra", "rsvd", "Rtsne", "S4Arrays", "S4Vectors", "S7", "sass", "ScaledMatrix", "scales", "scattermore", "scran", "sctransform", "scuttle", "Seqinfo", "Seurat", "SeuratObject", "shiny", "Signac", "SingleCellExperiment", "sitmo", "snow", "sourcetools", "sp", "spam", "SparseArray", "sparseMatrixStats", "spatstat.data", "spatstat.explore", "spatstat.geom", "spatstat.random", "spatstat.sparse", "spatstat.univar", "spatstat.utils", "statmod", "stringi", "stringr", "SummarizedExperiment", "survival", "sys", "tensor", "tibble", "tidyr", "tidyselect", "tinytex", "UCSC.utils", "utf8", "uwot", "vctrs", "viridisLite", "withr", "xfun", "xtable", "XVector", "yaml", "zoo" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "16-20260322-1ubuntu1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "MOSim.Rmd", "filename": "MOSim.html", "title": "Simulating bulk Multi-Omics Data with MOSim", "author": "Carolina Monzó, Carlos Martínez, Sonia Tarazona", "engine": "knitr::rmarkdown", "headings": [ "mosim", "Abstract", "Introduction", "Getting started", "MOSim input parameters", "Running the simulation:", "Provided STATegra dataset", "Providing custom data: omicData", "Changing omic settings: omicSim", "Working with simulation results", "The simulation object", "Retrieving the simulation settings: omicSettings", "Accessing the count data matrices: omicResults", "Obtaining the experimental design matrix: experimentalDesign", "Plotting results: plotProfile", "Advanced use cases", "Negative binomial variance", "Transforming regulator data to 1/0 format", "Special simulation case: Transcription Factors", "How to cite MOSim" ], "created": "2017-05-24 08:44:47", "modified": "2025-03-27 09:25:36", "commits": 6 }, { "source": "scMOSim.Rmd", "filename": "scMOSim.html", "title": "Simulating Single-Cell Multi-Omics Data with MOSim", "author": "Carolina Monzó, Ángeles Arzalluz-Luque, Sonia Tarazona", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Simulating Single-Cell Multi-Omics Data", "Data Preparation", "Providing Custom Data", "Running the Simulation: sc_mosim", "Default sc_mosim Simulation", "Customizing the sc_mosim Simulation", "Working with Simulation Results", "The sc_mosim Simulation Object", "Retrieving Simulation Settings", "Accessing the Count Data Matrices", "How to cite MOSim" ], "created": "2023-07-21 23:28:14", "modified": "2025-04-02 06:45:04", "commits": 16 } ], "_score": 6.90655051910145, "_indexed": true, "_nocasepkg": "mosim", "_universes": [ "bioc", "soniatarazona", "conesalab" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.9.0", "date": "2026-11-01T14:10:47.000Z", "distro": "resolute", "arch": "aarch64", "commit": "76f9819e904131dc41b557a19b25a5921dfcdd7a", "fileid": "https://r2.ropensci.org/f3e1bbdcb355bf6116ce6d18c8b0626cb4b98c7156f631eca05579134a81d5de", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310238613" }, { "r": "4.7.0", "os": "linux", "version": "2.9.0", "date": "2026-11-01T14:30:55.000Z", "distro": "resolute", "arch": "x86_64", "commit": "76f9819e904131dc41b557a19b25a5921dfcdd7a", "fileid": "https://r2.ropensci.org/f9e0cab8d0b853763fa1c963435a251a50d15d26225a204f036240cfec8a9f6f", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310238613" }, { "r": "4.6.2", "os": "linux", "version": "2.9.0", "date": "2026-11-01T14:10:01.000Z", "distro": "resolute", "arch": "aarch64", "commit": "76f9819e904131dc41b557a19b25a5921dfcdd7a", "fileid": "https://r2.ropensci.org/a245b4603244fdea0f10db0a3f0f67bcbc59f976c275185e931d9e125201cff9", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310238613" }, { "r": "4.6.2", "os": "linux", "version": "2.9.0", "date": "2026-11-01T14:30:55.000Z", "distro": "resolute", "arch": "x86_64", "commit": "76f9819e904131dc41b557a19b25a5921dfcdd7a", "fileid": "https://r2.ropensci.org/416288685c0a976c68d0b3e4d1928e98f3ada2f1ad867e6599c3d39d9b0c8bab", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310238613" }, { "r": "4.5.3", "os": "mac", "version": "2.9.0", "date": "2026-11-01T16:48:36.000Z", "arch": "aarch64", "commit": "76f9819e904131dc41b557a19b25a5921dfcdd7a", "fileid": "https://r2.ropensci.org/42ac2e10a3ecda4871fb06f259770a861d3f03ead23bfb620b574eedd501dbb3", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310238613" }, { "r": "4.5.3", "os": "mac", "version": "2.9.0", "date": "2026-11-01T16:43:45.000Z", "arch": "x86_64", "commit": "76f9819e904131dc41b557a19b25a5921dfcdd7a", "fileid": "https://r2.ropensci.org/305c9227c9127aff0166540af04d58e66aee0858c04fd955d43bf11c7a23bc77", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310238613" }, { "r": "4.6.2", "os": "mac", "version": "2.9.0", "date": "2026-11-01T16:49:19.000Z", "arch": "aarch64", "commit": "76f9819e904131dc41b557a19b25a5921dfcdd7a", "fileid": "https://r2.ropensci.org/8b0f46b746cbbdf8afb0894f413c8e1e58a3727824d949fbb9b22cffb98c04d0", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310238613" }, { "r": "4.6.2", "os": "mac", "version": "2.9.0", "date": "2026-11-01T16:42:39.000Z", "arch": "x86_64", "commit": "76f9819e904131dc41b557a19b25a5921dfcdd7a", "fileid": "https://r2.ropensci.org/80b2b4f85568eeb618f226878e20f90016835e718a5bf9612263ab130a3fbcdb", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310238613" }, { "r": "4.6.0", "os": "wasm", "version": "2.9.0", "date": "2026-11-01T14:29:37.000Z", "arch": "emscripten", "commit": "76f9819e904131dc41b557a19b25a5921dfcdd7a", "fileid": "https://r2.ropensci.org/19cf3d0078c34d06413d934defe2ea894a9356f6baed05cf9842af3eeb962ac3", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310238613" }, { "r": "4.7.0", "os": "win", "version": "2.9.0", "date": "2026-11-01T14:11:04.000Z", "arch": "aarch64", "commit": "76f9819e904131dc41b557a19b25a5921dfcdd7a", "fileid": "https://r2.ropensci.org/a1941963858e642743ce85600fbbff6715561fb64c2e406b6b0c5e120ab52db0", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310238613" }, { "r": "4.7.0", "os": "win", "version": "2.9.0", "date": "2026-11-01T14:09:30.000Z", "arch": "x86_64", "commit": "76f9819e904131dc41b557a19b25a5921dfcdd7a", "fileid": "https://r2.ropensci.org/cea674a1b6ac2fea5ce97cc4c2f3f5f07cb9fd8ec6693a4b1fe91687f472ec48", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310238613" }, { "r": "4.5.3", "os": "win", "version": "2.9.0", "date": "2026-11-01T14:09:14.000Z", "arch": "x86_64", "commit": "76f9819e904131dc41b557a19b25a5921dfcdd7a", "fileid": "https://r2.ropensci.org/da8dc858b0e1b09b3072ef419c86759c63ccd9ec15a7d3820914b1319d027038", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310238613" }, { "r": "4.6.2", "os": "win", "version": "2.9.0", "date": "2026-11-01T14:11:09.000Z", "arch": "aarch64", "commit": "76f9819e904131dc41b557a19b25a5921dfcdd7a", "fileid": "https://r2.ropensci.org/9db9378707c535763b6de9b0f46951b412d6c6d714f0926c65f2d26e242dac58", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310238613" }, { "r": "4.6.2", "os": "win", "version": "2.9.0", "date": "2026-11-01T14:09:33.000Z", "arch": "x86_64", "commit": "76f9819e904131dc41b557a19b25a5921dfcdd7a", "fileid": "https://r2.ropensci.org/a1c17ba6c5ac1693b0d587dd82d6bcb001deb4fc93846bd9d6fc99b37b68b2cd", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310238613" } ] }