{ "_id": "6a196068acfb0bcc41de58fb", "Package": "CIMICE", "Type": "Package", "Title": "CIMICE-R: (Markov) Chain Method to Inferr Cancer Evolution", "Version": "1.21.0", "Authors@R": "c(\nperson(\"Nicolò\", \"Rossi\",\nrole=c(\"aut\", \"cre\"), email=\"olocin.issor@gmail.com\",\ncomment = c(\"Lab. of Computational Biology and Bioinformatics, Department of Mathematics, Computer Science and Physics, University of Udine\",ORCID = \"0000-0002-6353-7396\"))\n)", "Description": "CIMICE is a tool in the field of tumor phylogenetics and\nits goal is to build a Markov Chain (called Cancer Progression\nMarkov Chain, CPMC) in order to model tumor subtypes evolution.\nThe input of CIMICE is a Mutational Matrix, so a boolean matrix\nrepresenting altered genes in a collection of samples. These\nsamples are assumed to be obtained with single-cell DNA\nanalysis techniques and the tool is specifically written to use\nthe peculiarities of this data for the CMPC construction.", "License": "Artistic-2.0", "Encoding": "UTF-8", "RoxygenNote": "7.1.2", "VignetteBuilder": "knitr", "biocViews": "Software, BiologicalQuestion, NetworkInference,\nResearchField, Phylogenetics, StatisticalMethod,\nGraphAndNetwork, Technology, SingleCell", "BugReports": "https://github.com/redsnic/CIMICE/issues", "URL": "https://github.com/redsnic/CIMICE", "BiocType": "Software", "Config/pak/sysreqs": "cmake libfontconfig1-dev libfreetype6-dev\nlibglpk-dev make libbz2-dev libicu-dev liblzma-dev libuv1-dev\nlibxml2-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:55:26 UTC", "RemoteUrl": "https://github.com/bioc/CIMICE", "RemoteRef": "HEAD", "RemoteSha": "57344c846b0a08505194acdb7fd2b6f0589d7bc8", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-29 08:17:21 UTC", "User": "root" }, "Author": "Nicolò Rossi [aut, cre] (Lab. of Computational Biology and\nBioinformatics, Department of Mathematics, Computer Science and\nPhysics, University of Udine, ORCID:\n)", "Maintainer": "Nicolò Rossi ", "MD5sum": "721cd1e598e61156ed941e93a85c4b01", "_user": "bioc", "_type": "src", "_file": "CIMICE_1.21.0.tar.gz", "_fileid": "631717d1556714ab013e3d7daa7fa24f767889657c307aefd0275956d6e4733c", "_filesize": 1202933, "_sha256": "631717d1556714ab013e3d7daa7fa24f767889657c307aefd0275956d6e4733c", "_created": "2026-05-29T08:17:21.000Z", "_published": "2026-05-29T09:46:16.719Z", "_jobs": [ { "job": 78464012524, "time": 165, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7286279613" }, { "job": 78464012482, "time": 231, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7286298517" }, { "job": 78464012504, "time": 297, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7286318521" }, { "job": 78464012493, "time": 221, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7287819755" }, { "job": 78464012481, "time": 263, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7287829419" }, { "job": 78463512945, "time": 212, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7286230985" }, { "job": 78464012511, "time": 144, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7286273257" }, { "job": 78464012485, "time": 484, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7286377810" }, { "job": 78464012596, "time": 456, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7286369117" }, { "job": 78464012487, "time": 522, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7286389347" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 7 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26626207608", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/CIMICE", "_commit": { "id": "57344c846b0a08505194acdb7fd2b6f0589d7bc8", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380926 }, "_maintainer": { "name": "Nicolò Rossi", "email": "olocin.issor@gmail.com", "orcid": "0000-0002-6353-7396" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "dplyr", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "glue", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "igraph", "role": "Imports" }, { "package": "networkD3", "role": "Imports" }, { "package": "visNetwork", "role": "Imports" }, { "package": "ggcorrplot", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "ggraph", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "maftools", "role": "Imports" }, { "package": "assertthat", "role": "Imports" }, { "package": "tidygraph", "role": "Imports" }, { "package": "expm", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "webshot", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.21.0", "bioc": "3.24" }, { "branch": "release", "version": "1.20.0", "bioc": "3.23" } ], "_topics": [ "software", "biologicalquestion", "networkinference", "researchfield", "phylogenetics", "statisticalmethod", "graphandnetwork", "technology", "singlecell" ], "_stars": 0, "_contributors": [ { "user": "redsnic", "count": 3179, "uuid": 5359908 }, { "user": "nturaga", "count": 118, "uuid": 2746443 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 340, "source": "https://www.bioconductor.org/packages/stats/bioc/CIMICE" }, "_devurl": "https://github.com/redsnic/cimice", "_searchresults": 5, "_rbuild": "4.6.0", "_assets": [ "extra/CIMICE.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/redsnic/cimice", "_realowner": "bioc", "_cranurl": false, "_exports": [ "annotate_mutational_matrix", "binary_radix_sort", "build_subset_graph", "build_topology_subset", "chunk_reader", "compact_dataset", "compute_weights_default", "computeDWNW", "computeUPW", "corrplot_from_mutational_matrix", "corrplot_genes", "corrplot_samples", "dataset_preprocessing", "dataset_preprocessing_population", "draw_ggraph", "draw_networkD3", "draw_visNetwork", "example_dataset", "example_dataset_withFreqs", "finalize_generator", "fix_clonal_genotype", "format_labels", "gene_mutations_hist", "get_no_of_children", "graph_non_transitive_subset_topology", "make_dataset", "make_generator_stub", "make_labels", "normalizeDWNW", "normalizeUPW", "perturb_dataset", "plot_generator", "prepare_generator_edge_set_command", "prepare_labels", "quick_run", "read", "read_CAPRI", "read_CAPRI_string", "read_CAPRIpop", "read_CAPRIpop_string", "read_MAF", "read_matrix", "remove_transitive_edges", "sample_mutations_hist", "select_genes_on_mutations", "select_samples_on_mutations", "set_generator_edges", "simulate_generator", "to_dot", "update_df" ], "_help": [ { "page": "annotate_mutational_matrix", "title": "Add samples and genes names to a mutational matrix", "topics": [ "annotate_mutational_matrix" ] }, { "page": "binary_radix_sort", "title": "Radix sort for a binary matrix", "topics": [ "binary_radix_sort" ] }, { "page": "build_subset_graph", "title": "Remove transitive edges and prepare graph", "topics": [ "build_subset_graph" ] }, { "page": "build_topology_subset", "title": "Compute subset relation as edge list", "topics": [ "build_topology_subset" ] }, { "page": "chunk_reader", "title": "Gradually read a file from disk", "topics": [ "chunk_reader" ] }, { "page": "CIMICE", "title": "CIMICE Package", "topics": [ "CIMICE" ] }, { "page": "compact_dataset", "title": "Compact dataset rows", "topics": [ "compact_dataset" ] }, { "page": "compute_weights_default", "title": "Compute default weights", "topics": [ "compute_weights_default" ] }, { "page": "computeDWNW", "title": "Down weights computation", "topics": [ "computeDWNW" ] }, { "page": "computeDWNW_aux", "title": "Down weights computation (aux)", "topics": [ "computeDWNW_aux" ] }, { "page": "computeUPW", "title": "Up weights computation", "topics": [ "computeUPW" ] }, { "page": "computeUPW_aux", "title": "Up weights computation (aux)", "topics": [ "computeUPW_aux" ] }, { "page": "corrplot_from_mutational_matrix", "title": "Correlation plot from mutational matrix", "topics": [ "corrplot_from_mutational_matrix" ] }, { "page": "corrplot_genes", "title": "Gene based correlation plot", "topics": [ "corrplot_genes" ] }, { "page": "corrplot_samples", "title": "Sample based correlation plot", "topics": [ "corrplot_samples" ] }, { "page": "dataset_preprocessing", "title": "Run CIMICE preprocessing", "topics": [ "dataset_preprocessing" ] }, { "page": "dataset_preprocessing_population", "title": "Run CIMICE preprocessing for poulation format dataset", "topics": [ "dataset_preprocessing_population" ] }, { "page": "draw_ggraph", "title": "ggplot graph output", "topics": [ "draw_ggraph" ] }, { "page": "draw_networkD3", "title": "NetworkD3 graph output", "topics": [ "draw_networkD3" ] }, { "page": "draw_visNetwork", "title": "VisNetwork graph output (default)", "topics": [ "draw_visNetwork" ] }, { "page": "example_dataset", "title": "Creates a simple example dataset", "topics": [ "example_dataset" ] }, { "page": "example_dataset_withFreqs", "title": "Creates a simple example dataset with frequency column", "topics": [ "example_dataset_withFreqs" ] }, { "page": "finalize_generator", "title": "Finalize generator normalizing edge weights", "topics": [ "finalize_generator" ] }, { "page": "fix_clonal_genotype", "title": "Manage Clonal genotype in data", "topics": [ "fix_clonal_genotype" ] }, { "page": "format_labels", "title": "Format labels for output object", "topics": [ "format_labels" ] }, { "page": "gene_mutations_hist", "title": "Histogram of genes' frequencies", "topics": [ "gene_mutations_hist" ] }, { "page": "get_no_of_children", "title": "Get number of children", "topics": [ "get_no_of_children" ] }, { "page": "graph_non_transitive_subset_topology", "title": "Default preparation of graph topology", "topics": [ "graph_non_transitive_subset_topology" ] }, { "page": "make_dataset", "title": "Dataset line by line construction: initialization", "topics": [ "make_dataset" ] }, { "page": "make_generator_stub", "title": "Create a stub for a generator", "topics": [ "make_generator_stub" ] }, { "page": "make_labels", "title": "Helper function to create labels", "topics": [ "make_labels" ] }, { "page": "normalizeDWNW", "title": "Down weights normalization", "topics": [ "normalizeDWNW" ] }, { "page": "normalizeUPW", "title": "Up weights normalization", "topics": [ "normalizeUPW" ] }, { "page": "perturb_dataset", "title": "Perturbate a boolean matrix", "topics": [ "perturb_dataset" ] }, { "page": "plot_generator", "title": "Plot a generator", "topics": [ "plot_generator" ] }, { "page": "prepare_generator_edge_set_command", "title": "Prepare a command to add edge weights to a generator", "topics": [ "prepare_generator_edge_set_command" ] }, { "page": "prepare_labels", "title": "Prepare node labels based on genotypes", "topics": [ "prepare_labels" ] }, { "page": "quick_run", "title": "Run CIMICE defaults", "topics": [ "quick_run" ] }, { "page": "read", "title": "Read a \"CAPRI\" file", "topics": [ "read" ] }, { "page": "read_CAPRI", "title": "Read a \"CAPRI\" file", "topics": [ "read_CAPRI" ] }, { "page": "read_CAPRI_string", "title": "Read \"CAPRI\" file from a string", "topics": [ "read_CAPRI_string" ] }, { "page": "read_CAPRIpop", "title": "Read a \"CAPRIpop\" file", "topics": [ "read_CAPRIpop" ] }, { "page": "read_CAPRIpop_string", "title": "Read \"CAPRIpop\" file from a string", "topics": [ "read_CAPRIpop_string" ] }, { "page": "read_MAF", "title": "Create mutational matrix from MAF file", "topics": [ "read_MAF" ] }, { "page": "read_matrix", "title": "Read dataset from an R matrix", "topics": [ "read_matrix" ] }, { "page": "remove_transitive_edges", "title": "Remove transitive edges from an edgelist", "topics": [ "remove_transitive_edges" ] }, { "page": "sample_mutations_hist", "title": "Histogram of samples' frequencies", "topics": [ "sample_mutations_hist" ] }, { "page": "select_genes_on_mutations", "title": "Filter dataset by genes' mutation count", "topics": [ "select_genes_on_mutations" ] }, { "page": "select_samples_on_mutations", "title": "Filter dataset by samples' mutation count", "topics": [ "select_samples_on_mutations" ] }, { "page": "set_generator_edges", "title": "Add edge weights to a generator", "topics": [ "set_generator_edges" ] }, { "page": "simulate_generator", "title": "Create datasets from generators", "topics": [ "simulate_generator" ] }, { "page": "to_dot", "title": "Dot graph output", "topics": [ "to_dot" ] }, { "page": "update_df", "title": "Dataset line by line construction: add a sample", "topics": [ "update_df" ] } ], "_readme": "https://github.com/bioc/CIMICE/raw/HEAD/README.md", "_rundeps": [ "assertthat", "base64enc", "bslib", "cachem", "cli", "cpp11", "data.table", "data.tree", "digest", "DNAcopy", "dplyr", "evaluate", "expm", "farver", "fastmap", "fontawesome", "fs", "generics", "ggcorrplot", "ggforce", "ggplot2", "ggraph", "ggrepel", "glue", "graphlayouts", "gridExtra", "gtable", "highr", "htmltools", "htmlwidgets", "igraph", "isoband", "jquerylib", "jsonlite", "knitr", "labeling", "lattice", "lifecycle", "maftools", "magrittr", "MASS", "Matrix", "memoise", "mime", "networkD3", "pheatmap", "pillar", "pkgconfig", "plyr", "polyclip", "purrr", "R6", "rappdirs", "RColorBrewer", "Rcpp", "RcppArmadillo", "reshape2", "Rhtslib", "rlang", "rmarkdown", "S7", "sass", "scales", "stringi", "stringr", "survival", "systemfonts", "tibble", "tidygraph", "tidyr", "tidyselect", "tinytex", "tweenr", "utf8", "vctrs", "viridis", "viridisLite", "visNetwork", "withr", "xfun", "yaml" ], "_vignettes": [ { "source": "CIMICER.Rmd", "filename": "CIMICER.html", "title": "CIMICE-R: (Markov) Chain Method to Infer Cancer Evolution", "author": "Nicolò Rossi", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Used libraries", "Input management", "Preliminary check of mutations distributions", "Simple procedures of feature selection", "By genes", "By samples", "Both selections", "Correlation plot", "Group equal genotypes", "Graph topology construction", "Graph weight computation", "\"UP\" weights", "\"UP\" weights normalization", "\"DOWN\" Weights", "\"DOWN\" weights normalization", "Output presentation", "Session information" ], "created": "2021-08-03 21:19:14", "modified": "2022-03-12 13:42:49", "commits": 3 }, { "source": "CIMICE_SHORT.Rmd", "filename": "CIMICE_SHORT.html", "title": "Quick guide", "author": "Nicolò Rossi", "engine": "knitr::rmarkdown", "headings": [ "Reference for quick CIMICE analysis", "Read input", "Preprocess dataset", "Build topology", "Compute Weights", "Visualize output:" ], "created": "2020-11-24 10:54:58", "modified": "2021-07-07 12:04:25", "commits": 4 } ], "_score": 4.301029995663981, "_indexed": true, "_nocasepkg": "cimice", "_universes": [ "bioc", "redsnic" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.21.0", "date": "2026-05-29T08:20:39.000Z", "distro": "noble", "commit": "57344c846b0a08505194acdb7fd2b6f0589d7bc8", "fileid": "9229e410f0907a6972dd7ce3204319e748e7d81aec5cbc7725b584943277191e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626207608" }, { "r": "4.6.0", "os": "linux", "version": "1.21.0", "date": "2026-05-29T08:21:55.000Z", "distro": "noble", "commit": "57344c846b0a08505194acdb7fd2b6f0589d7bc8", "fileid": "097a861eb78c682198d0d6d3998106ba510a1f29babde08454d0eaccdae69908", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626207608" }, { "r": "4.5.3", "os": "mac", "version": "1.21.0", "date": "2026-05-29T09:44:43.000Z", "commit": "57344c846b0a08505194acdb7fd2b6f0589d7bc8", "fileid": "4fbba7f25736de03d15e3d05cd979337e855fd2e442cf4a65f2d0e1bd4c88953", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626207608" }, { "r": "4.6.0", "os": "mac", "version": "1.21.0", "date": "2026-05-29T09:45:10.000Z", "commit": "57344c846b0a08505194acdb7fd2b6f0589d7bc8", "fileid": "2d4c91bf2a9c3a4fb77b555865f1f991a1d02b2c04fcac4c2c1ee8666042502b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626207608" }, { "r": "4.6.0", "os": "wasm", "version": "1.21.0", "date": "2026-05-29T08:20:05.000Z", "commit": "57344c846b0a08505194acdb7fd2b6f0589d7bc8", "fileid": "509bec9f98d66c46b18545c6a3eed1aa698d6533a0c4990e4cdd24a0efa23c9c", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626207608" }, { "r": "4.7.0", "os": "win", "version": "1.21.0", "date": "2026-05-29T08:24:37.000Z", "commit": "57344c846b0a08505194acdb7fd2b6f0589d7bc8", "fileid": "f2df626d5fc37f3b700aa0e90855dc53245da6d594e8956be299d5a508f5c620", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626207608" }, { "r": "4.5.3", "os": "win", "version": "1.21.0", "date": "2026-05-29T08:24:15.000Z", "commit": "57344c846b0a08505194acdb7fd2b6f0589d7bc8", "fileid": "99268879851ea00a62dcda6149cc2da36b4a688e212f894f903dcee16d0d5dac", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626207608" }, { "r": "4.6.0", "os": "win", "version": "1.21.0", "date": "2026-05-29T08:25:22.000Z", "commit": "57344c846b0a08505194acdb7fd2b6f0589d7bc8", "fileid": "a9b917373db00e274985bd7d57caa29720f1c5714b1d480e2de95bf1814b6907", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626207608" } ] }