{ "_id": "6a107286acfb0bcc41cabf9d", "Package": "WormTensor", "Type": "Package", "Title": "A Clustering Method for Time-Series Whole-Brain Activity Data of\n'C. elegans'", "Version": "0.1.2", "Authors@R": "c(person(\"Kentaro\", \"Yamamoto\", role = c(\"aut\", \"cre\"),\nemail = \"yamaken37.the.answer@gmail.com\"),\nperson(\"Koki\", \"Tsuyuzaki\", role = \"aut\"),\nperson(\"Itoshi\", \"Nikaido\", role = \"aut\"))", "Maintainer": "Kentaro Yamamoto ", "Description": "A toolkit to detect clusters from distance matrices. The\ndistance matrices are assumed to be calculated between the\ncells of multiple animals ('Caenorhabditis elegans') from input\ntime-series matrices. Some functions for generating distance\nmatrices, performing clustering, evaluating the clustering, and\nvisualizing the results of clustering and evaluation are\navailable. We're also providing the download function to\nretrieve the calculated distance matrices from 'figshare'\n.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "URL": "https://github.com/rikenbit/WormTensor", "BugReports": "https://github.com/rikenbit/WormTensor/issues", "Config/testthat/edition": "3", "RoxygenNote": "7.2.0", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev zlib1g-dev", "Repository": "https://rikenbit.r-universe.dev", "Date/Publication": "2025-07-21 16:25:58 UTC", "RemoteUrl": "https://github.com/rikenbit/wormtensor", "RemoteRef": "HEAD", "RemoteSha": "6cf63a315d3fe51e9aac83fc95e4b6b27b040791", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-07 06:21:49 UTC", "User": "root" }, "Author": "Kentaro Yamamoto [aut, cre],\nKoki Tsuyuzaki [aut],\nItoshi Nikaido [aut]", "MD5sum": "9b4506aa90166be36fe145d52acceaaf", "_user": "rikenbit", "_type": "src", "_file": "WormTensor_0.1.2.tar.gz", "_fileid": "3001468e93eb02da2c3a5f6c6f55c040ef9f853aea46ad22b9595ae2109e6e52", "_filesize": 3961352, "_sha256": "3001468e93eb02da2c3a5f6c6f55c040ef9f853aea46ad22b9595ae2109e6e52", "_created": "2026-05-07T06:21:49.000Z", "_published": "2026-05-22T15:13:10.594Z", "_distro": "noble", "_jobs": [ { "job": 77407886952, "time": 270, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "6848312821" }, { "job": 77407886761, "time": 300, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "6848322221" }, { "job": 77407886962, "time": 179, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "6848343211" }, { "job": 77407886860, "time": 216, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "6848340249" }, { "job": 77407886128, "time": 337, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "6848244240" }, { "job": 77407886299, "time": 166, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7163923808" }, { "job": 77407887011, "time": 224, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "6848301755" }, { "job": 77407887186, "time": 274, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "6848313641" }, { "job": 77407886847, "time": 222, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "6848301246" } ], "_buildurl": "https://github.com/r-universe/rikenbit/actions/runs/25479276637", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/rikenbit/wormtensor", "_commit": { "id": "6cf63a315d3fe51e9aac83fc95e4b6b27b040791", "author": "yamaken37 ", "committer": "yamaken37 ", "message": "Merge branch 'master' of https://github.com/rikenbit/WormTensor\n", "time": 1753115158 }, "_maintainer": { "name": "Kentaro Yamamoto", "email": "yamaken37.the.answer@gmail.com" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "rTensor", "role": "Imports" }, { "package": "usedist", "role": "Imports" }, { "package": "dtwclust", "role": "Imports" }, { "package": "clusterSim", "role": "Imports" }, { "package": "clValid", "role": "Imports" }, { "package": "aricode", "role": "Imports" }, { "package": "cluster", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "Rtsne", "role": "Imports" }, { "package": "uwot", "role": "Imports" }, { "package": "factoextra", "role": "Imports" }, { "package": "ggrepel", "role": "Imports" }, { "package": "cowplot", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "rikenbit", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-30", "n": 2 } ], "_tags": [], "_stars": 1, "_contributors": [ { "user": "yamaken37", "count": 127, "uuid": 58546728 } ], "_userbio": { "uuid": 7158513, "type": "organization", "name": "RIKEN BiT", "description": "Omics AI Research Team, Advanced General Intelligence in Science Program (AGIS), TRIP, RIKEN (ex-Laboratory for Bioinformatics Research, RIKEN)" }, "_downloads": { "count": 205, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/WormTensor" }, "_devurl": "https://github.com/rikenbit/wormtensor", "_searchresults": 3, "_rbuild": "4.6.0", "_assets": [ "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", "extra/WormTensor.html", "manual.pdf" ], "_homeurl": "https://github.com/rikenbit/wormtensor", "_realowner": "rikenbit", "_cranurl": true, "_releases": [ { "version": "0.1.0", "date": "2022-09-08" }, { "version": "0.1.1", "date": "2024-07-23" }, { "version": "0.1.2", "date": "2025-07-21" } ], "_exports": [ "as_worm_tensor", "worm_clustering", "worm_distance", "worm_download", "worm_evaluate", "worm_membership", "worm_visualize" ], "_help": [ { "page": "AllGenerics_component", "title": "Components for WormTensor object", "topics": [ "AllGenerics_component", "worm_clustering", "worm_evaluate", "worm_membership", "worm_visualize" ] }, { "page": "as_worm_tensor", "title": "Generates WormTensor object A WormTensor object is generated from distance matrices.", "topics": [ "as_worm_tensor" ] }, { "page": "worm_clustering-WormTensor-method", "title": "Generates clustering result A clustering result is generated from a membership tensor.", "topics": [ "worm_clustering,WormTensor-method" ] }, { "page": "worm_distance", "title": "Generates distance matrices Distance matrices are generated between the cells of multiple animals (Caenorhabditis elegans) from time-series matrices.", "topics": [ "worm_distance" ] }, { "page": "worm_download", "title": "Downloads distance matrices 28 animals' data including 24 normal and 4 noisy are retrieved from figshare.", "topics": [ "worm_download" ] }, { "page": "worm_evaluate-WormTensor-method", "title": "Evaluates clustering result An evaluation result is generated from a WormTensor object.", "topics": [ "worm_evaluate,WormTensor-method" ] }, { "page": "worm_membership-WormTensor-method", "title": "Generates membership tensor A membership tensor is generated from distance matrices.", "topics": [ "worm_membership,WormTensor-method" ] }, { "page": "worm_visualize-WormTensor-method", "title": "Plots evaluation result A visualization result is generated from a WormTensor object.", "topics": [ "worm_visualize,WormTensor-method" ] }, { "page": "WormTensor-class", "title": "S4 class used by as_worm_tensor.R, worm_membership.R, worm_clustering.R, worm_evaluate.R, worm_visualize.R", "topics": [ "WormTensor-class" ] } ], "_readme": "https://github.com/rikenbit/wormtensor/raw/HEAD/README.md", "_rundeps": [ "abind", "ade4", "aricode", "backports", "base64enc", "BH", "boot", "broom", "bslib", "cachem", "car", "carData", "class", "cli", "clue", "cluster", "clusterSim", "clValid", "codetools", "colorspace", "commonmark", "corrplot", "cowplot", "cpp11", "crosstalk", "dendextend", "Deriv", "digest", "doBy", "dplyr", "dqrng", "DT", "dtw", "dtwclust", "e1071", "ellipse", "emmeans", "estimability", "evaluate", "factoextra", "FactoMineR", "farver", "fastmap", "flashClust", "flexclust", "FNN", "fontawesome", "foreach", "forecast", "Formula", "fracdiff", "fs", "generics", "ggplot2", "ggpubr", "ggrepel", "ggsci", "ggsignif", "glue", "gridExtra", "gtable", "highr", "htmltools", "htmlwidgets", "httpuv", "irlba", "isoband", "iterators", "jquerylib", "jsonlite", "knitr", "labeling", "later", "lattice", "lazyeval", "leaps", "lifecycle", "lme4", "lmtest", "magrittr", "MASS", "Matrix", "MatrixModels", "memoise", "mgcv", "microbenchmark", "mime", "minqa", "modelr", "modeltools", "multcompView", "mvtnorm", "nlme", "nloptr", "nnet", "numDeriv", "otel", "pbkrtest", "pillar", "pixmap", "pkgconfig", "plyr", "polynom", "promises", "proxy", "purrr", "quantreg", "R6", "rappdirs", "rbibutils", "RColorBrewer", "Rcpp", "RcppAnnoy", "RcppArmadillo", "RcppEigen", "RcppParallel", "RcppProgress", "RcppThread", "Rdpack", "reformulas", "reshape2", "rlang", "rmarkdown", "RSpectra", "rstatix", "rTensor", "Rtsne", "S7", "sass", "scales", "scatterplot3d", "shiny", "shinyjs", "sitmo", "sourcetools", "sp", "SparseM", "stringi", "stringr", "survival", "tibble", "tidyr", "tidyselect", "timeDate", "tinytex", "urca", "usedist", "utf8", "uwot", "vctrs", "viridis", "viridisLite", "withr", "xfun", "xtable", "yaml", "zoo" ], "_vignettes": [ { "source": "WormTensor.Rmd", "filename": "WormTensor.html", "title": "Clustering and visualization of time-series whole-brain activity data of C. elegans using WormTensor", "author": "Kentaro Yamamoto, Koki Tsuyuzaki, Itoshi Nikaido", "engine": "knitr::rmarkdown", "headings": [ "Load libraries", "worm_download", "as_worm_tensor", "worm_membership", "worm_clustering", "worm_evaluate", "worm_visualize`", "Pipe Operation", "Pipe Operation (with Labels)", "worm_distance", "Session Information" ], "created": "2022-08-03 04:26:37", "modified": "2022-08-25 05:23:07", "commits": 9 } ], "_score": 3.6989700043360187, "_indexed": true, "_nocasepkg": "wormtensor", "_universes": [ "rikenbit" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.1.2", "date": "2026-05-07T06:24:40.000Z", "distro": "noble", "commit": "6cf63a315d3fe51e9aac83fc95e4b6b27b040791", "fileid": "070973a2acfafc41ecffc0c6f1a3b42169b1356a9a526eb74f2a8b79b75c3978", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rikenbit/actions/runs/25479276637" }, { "r": "4.6.0", "os": "linux", "version": "0.1.2", "date": "2026-05-07T06:25:08.000Z", "distro": "noble", "commit": "6cf63a315d3fe51e9aac83fc95e4b6b27b040791", "fileid": "173d38252a2ef366eea865604e5e65799fc6fb275c4c65481fd7ce588258ba58", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rikenbit/actions/runs/25479276637" }, { "r": "4.5.3", "os": "mac", "version": "0.1.2", "date": "2026-05-07T06:27:08.000Z", "commit": "6cf63a315d3fe51e9aac83fc95e4b6b27b040791", "fileid": "07037fc65079dd8997c207fbb438f56a4aaa4094f98d50337d252c44234b4433", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rikenbit/actions/runs/25479276637" }, { "r": "4.6.0", "os": "mac", "version": "0.1.2", "date": "2026-05-07T06:26:23.000Z", "commit": "6cf63a315d3fe51e9aac83fc95e4b6b27b040791", "fileid": "945c1a541f53eabc5f40cf971c8dfca4b3b558f3c3f560929186b5b59a41e57b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rikenbit/actions/runs/25479276637" }, { "r": "4.7.0", "os": "win", "version": "0.1.2", "date": "2026-05-07T06:23:46.000Z", "commit": "6cf63a315d3fe51e9aac83fc95e4b6b27b040791", "fileid": "f15019a49937740bb5a7e327a5b7435955105201363785cb0a4909e0db938ac1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rikenbit/actions/runs/25479276637" }, { "r": "4.5.3", "os": "win", "version": "0.1.2", "date": "2026-05-07T06:24:26.000Z", "commit": "6cf63a315d3fe51e9aac83fc95e4b6b27b040791", "fileid": "7ebf58e00840912d8cf044b8717ae2298f15af73ef81ed87d56e1fe92ee5d424", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rikenbit/actions/runs/25479276637" }, { "r": "4.6.0", "os": "win", "version": "0.1.2", "date": "2026-05-07T06:23:54.000Z", "commit": "6cf63a315d3fe51e9aac83fc95e4b6b27b040791", "fileid": "0cc729b796cfae2a7c08da0b22d751985fb252a4ea61f3fba6c1b724c221658d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rikenbit/actions/runs/25479276637" }, { "r": "4.6.0", "os": "wasm", "version": "0.1.2", "date": "2026-05-22T15:12:53.000Z", "commit": "6cf63a315d3fe51e9aac83fc95e4b6b27b040791", "fileid": "8b2952ed814ba058fdb82a0a6a6b0cc6ac83a8ff34977df4ea643385d85f1d74", "status": "success", "buildurl": "https://github.com/r-universe/rikenbit/actions/runs/25479276637" } ] }