{ "_id": "6acdf37ca14063b82c3ad68f", "Package": "segmenTier", "Type": "Package", "Title": "Similarity-Based Segmentation of Multidimensional Signals", "Version": "0.1.3", "Author": "Rainer Machne, Douglas B. Murray, Peter F. Stadler", "URL": "https://github.com/raim/segmenTier", "BugReports": "https://github.com/raim/segmenTier/issues", "Maintainer": "Rainer Machne ", "Description": "A dynamic programming solution to segmentation based on\nmaximization of arbitrary similarity measures within segments.\nThe general idea, theory and this implementation are described\nin Machne, Murray & Stadler (2017)\n. In addition to the core\nalgorithm, the package provides time-series processing and\nclustering functions as described in the publication. These are\ngenerally applicable where a `k-means` clustering yields\nmeaningful results, and have been specifically developed for\nclustering of the Discrete Fourier Transform of periodic gene\nexpression data (`circadian' or `yeast metabolic\noscillations'). This clustering approach is outlined in the\nsupplemental material of Machne & Murray (2012)\n), and here is used as a\nbasis of segment similarity measures. Notably, the time-series\nprocessing and clustering functions can also be used as\nstand-alone tools, independent of segmentation, e.g., for\ntranscriptome data already mapped to genes.", "License": "GPL (>= 2)", "Encoding": "UTF-8", "RoxygenNote": "7.3.2", "VignetteBuilder": "knitr", "Repository": "https://raim.r-universe.dev", "Date/Publication": "2025-07-17 09:59:52 UTC", "RemoteUrl": "https://github.com/raim/segmentier", "RemoteRef": "HEAD", "RemoteSha": "91505fd75333466c9568b66112b037a7cdd09b73", "RemoteSubdir": "pkg", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-10-13 08:45:56 UTC", "User": "root" }, "_user": "raim", "_type": "src", "_file": "segmenTier_0.1.3.tar.gz", "_fileid": "https://r2.ropensci.org/1d416df0b871a741a2a0f2ad76fff72c1b8bd645821c47cce042890c5d34cc8b", "_filesize": 948967, "_sha256": "1d416df0b871a741a2a0f2ad76fff72c1b8bd645821c47cce042890c5d34cc8b", "_expires": "2027-01-21T09:01:43.000Z", "_created": "2026-10-13T08:45:56.000Z", "_published": "2026-10-13T09:01:48.820Z", "_buildurl": "https://github.com/r-universe/raim/actions/runs/38371030858", "_status": "success", "_host": "GitHub-Actions", "_jobs": [ { "job": 115209527354, "time": 142, "config": "linux-devel-arm64", "r": "4.7.0", "check": "WARNING", "artifact": "11799550772" }, { "job": 115209527277, "time": 132, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "11798544880" }, { "job": 115209527524, "time": 126, "config": "linux-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "11799690657" }, { "job": 115209527366, "time": 130, "config": "linux-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "11799545773" }, { "job": 115209527575, "time": 124, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "11799403895" }, { "job": 115209527691, "time": 287, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "11799997796" }, { "job": 115209527444, "time": 113, "config": "macos-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "11799014111" }, { "job": 115209527431, "time": 312, "config": "macos-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "11799362326" }, { "job": 115207925442, "time": 244, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11799510642" }, { "job": 115209527379, "time": 129, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11799241653" }, { "job": 115209527541, "time": 219, "config": "windows-devel-arm64", "r": "4.7.0", "check": "WARNING", "artifact": "11799690943" }, { "job": 115209527486, "time": 164, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "11799820773" }, { "job": 115209527576, "time": 138, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "11799825806" }, { "job": 115209527534, "time": 221, "config": "windows-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "11799157847" }, { "job": 115209527676, "time": 173, "config": "windows-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "11799068355" } ], "_upstream": "https://github.com/raim/segmentier", "_commit": { "id": "91505fd75333466c9568b66112b037a7cdd09b73", "author": "raim ", "committer": "raim ", "message": "exporting new snr function, and ensuring dimnames\n", "time": 1752746392 }, "_maintainer": { "name": "Rainer Machne", "email": "raim@tbi.univie.ac.at", "login": "raim", "orcid": "0000-0002-1274-5099", "description": "theoretical biologist and experimental bioinformatician", "uuid": 729902 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "Rcpp", "role": "LinkingTo" }, { "package": "Rcpp", "version": ">= 0.12.7", "role": "Imports" }, { "package": "flowMerge", "role": "Suggests" }, { "package": "flowClust", "role": "Suggests" }, { "package": "flowCore", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "raim", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 3, "_contributors": [ { "user": "raim", "count": 659, "uuid": 729902 }, { "user": "ovpop100", "count": 3, "uuid": 18185854 } ], "_userbio": { "uuid": 729902, "type": "user", "name": "Rainer Machne", "followers": 18, "description": "theoretical biologist and experimental bioinformatician" }, "_downloads": { "count": 241, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/segmenTier" }, "_mentions": 2, "_devurl": "https://github.com/raim/segmentier", "_searchresults": 14, "_topics": [ "cpp" ], "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/readme.html", "extra/readme.md", "extra/segmenTier.html" ], "_homeurl": "https://github.com/raim/segmentier", "_realowner": "raim", "_cranurl": true, "_releases": [ { "version": "0.1.2", "date": "2019-02-18" } ], "_exports": [ "ash", "backtrace", "calculateScore", "clusterCor_c", "clusterTimeseries", "colorClusters", "flowclusterTimeseries", "get_snr", "log_1", "plotdev", "plotSegmentation", "processTimeseries", "segmentCluster.batch", "segmentClusters", "setVarySettings", "sortClusters" ], "_datasets": [ { "name": "tsd", "title": "Transcriptome time-series from budding yeast.", "object": "primseg436", "file": "primseg436.rda", "class": [ "matrix", "array" ], "fields": [ "TS_02", "TS_03", "TS_04", "TS_05", "TS_06", "TS_07", "TS_08", "TS_09", "TS_10", "TS_11", "TS_12", "TS_13", "TS_14", "TS_15", "TS_16", "TS_17", "TS_18", "TS_19", "TS_20", "TS_21", "TS_22", "TS_23", "TS_24", "TS_25" ], "rows": 7624, "table": true, "tojson": true } ], "_help": [ { "page": "ash", "title": "'asinh' data transformation", "topics": [ "ash" ] }, { "page": "backtrace", "title": "Back-tracing step of the 'segmenTier' algorithm.", "topics": [ "backtrace" ] }, { "page": "calculateScore", "title": "segmenTier's core dynamic programming routine in Rcpp", "topics": [ "calculateScore" ] }, { "page": "clusterCor_c", "title": "Calculates position-cluster correlations for scoring function \"icor\".", "topics": [ "clusterCor_c" ] }, { "page": "clusterTimeseries", "title": "Cluster a processed time-series with k-means.", "topics": [ "clusterTimeseries" ] }, { "page": "colorClusters", "title": "Assign colors to clusters.", "topics": [ "colorClusters" ] }, { "page": "flowclusterTimeseries", "title": "Cluster a processed time-series with 'flowClust' & 'flowMerge'.", "topics": [ "flowclusterTimeseries" ] }, { "page": "get_snr", "title": "Scale a DFT to a signal-to-noise ratio, where each frequency is divided by the mean of all other frequencies.", "topics": [ "get_snr" ] }, { "page": "log_1", "title": "log transformation handling zeros by adding 1", "topics": [ "log_1" ] }, { "page": "logLik.kmeans", "title": "Experimental: AIC/BIC for kmeans", "topics": [ "logLik.kmeans" ] }, { "page": "myPearson", "title": "Pearson product-moment correlation coefficient", "topics": [ "myPearson" ] }, { "page": "plot.clustering", "title": "Plot method for the \"clustering\" object.", "topics": [ "plot.clustering" ] }, { "page": "plot.segments", "title": "Plot method for the \"segments\" object.", "topics": [ "plot.segments" ] }, { "page": "plot.timeseries", "title": "Plot method for the \"timeseries\" object.", "topics": [ "plot.timeseries" ] }, { "page": "plotdev", "title": "Switch between plot devices.", "topics": [ "plotdev" ] }, { "page": "plotSegmentation", "title": "Summary plot for the 'segmenTier' pipeline.", "topics": [ "plotSegmentation" ] }, { "page": "print.segments", "title": "Print method for segmentation result from 'segmentClusters'.", "topics": [ "print.segments" ] }, { "page": "processTimeseries", "title": "Process a time-series for clustering and segmentation.", "topics": [ "processTimeseries" ] }, { "page": "segmentCluster.batch", "title": "Batch wrapper for 'segmentClusters'.", "topics": [ "segmentCluster.batch" ] }, { "page": "segmentClusters", "title": "Run the 'segmenTier' algorithm.", "topics": [ "segmentClusters" ] }, { "page": "segmenTier", "title": "segmenTier : cluster-based segmentation from a sequential clustering", "topics": [ "segmenTier" ] }, { "page": "setVarySettings", "title": "Parameters for 'segmentCluster.batch'.", "topics": [ "setVarySettings" ] }, { "page": "sortClusters", "title": "Sort clusters by similarity.", "topics": [ "sortClusters" ] }, { "page": "tsd", "title": "Transcriptome time-series from budding yeast.", "topics": [ "tsd" ] } ], "_readme": "https://github.com/raim/segmentier/raw/HEAD/README.md", "_rundeps": [ "Rcpp" ], "_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": "segmenTier.Rmd", "filename": "segmenTier.html", "title": "segmenTier: Similarity-Based Segmentation of Multi-Dimensional Signals", "author": "Rainer Machne, Douglas B. Murray, Peter F. Stadler", "engine": "knitr::rmarkdown", "headings": [ "Summary", "Theory & Implementation", "The Recursion", "The Scoring Functions", "Scaling & Nuisance Segments", "User-Defined Similarities", "Time-Series Processing & Clustering", "Package Outlook", "Usage", "Installation", "Quick Guide", "Demonstrations", "Demo I: Direct Interface to Algorithm", "Demo II: Clustering, Batch Segmentation & Parameter Scans", "Karl, the segmenTier", "References" ], "created": "2019-01-16 14:12:25", "modified": "2019-02-08 16:18:03", "commits": 29 } ], "_score": 4.623249290397901, "_indexed": true, "_nocasepkg": "segmentier", "_universes": [ "raim" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.1.3", "date": "2026-10-13T08:48:10.000Z", "distro": "resolute", "arch": "aarch64", "commit": "91505fd75333466c9568b66112b037a7cdd09b73", "fileid": "https://r2.ropensci.org/3b86d33f8f66f9c1dcbb4e9f734e591afc9b9639cfda120e57d11a7ee8f1c92f", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/raim/actions/runs/38371030858" }, { "r": "4.7.0", "os": "linux", "version": "0.1.3", "date": "2026-10-13T08:48:00.000Z", "distro": "resolute", "arch": "x86_64", "commit": "91505fd75333466c9568b66112b037a7cdd09b73", "fileid": "https://r2.ropensci.org/12ffaa7bcb9cc1237e5954601d473a0c3772dea47655671d68a5d46a2c5a3952", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/raim/actions/runs/38371030858" }, { "r": "4.6.1", "os": "linux", "version": "0.1.3", "date": "2026-10-13T08:47:58.000Z", "distro": "resolute", "arch": "aarch64", "commit": "91505fd75333466c9568b66112b037a7cdd09b73", "fileid": "https://r2.ropensci.org/014247e4cddd4b70091413e3e395673efb59f436ecb35c88e0bf54febe4a3cd2", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/raim/actions/runs/38371030858" }, { "r": "4.6.1", "os": "linux", "version": "0.1.3", "date": "2026-10-13T08:48:02.000Z", "distro": "resolute", "arch": "x86_64", "commit": "91505fd75333466c9568b66112b037a7cdd09b73", "fileid": "https://r2.ropensci.org/6daf6f30d03871e43ea9b298de71e65c77d6735f54aae5f00043bc18cac20d9d", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/raim/actions/runs/38371030858" }, { "r": "4.5.3", "os": "mac", "version": "0.1.3", "date": "2026-10-13T09:00:48.000Z", "arch": "aarch64", "commit": "91505fd75333466c9568b66112b037a7cdd09b73", "fileid": "https://r2.ropensci.org/bccba2fa97eac04a9c9f41850a7656323536a94c2dd0ff5ec9d3d360b6dd38c2", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/raim/actions/runs/38371030858" }, { "r": "4.5.3", "os": "mac", "version": "0.1.3", "date": "2026-10-13T08:54:37.000Z", "arch": "x86_64", "commit": "91505fd75333466c9568b66112b037a7cdd09b73", "fileid": "https://r2.ropensci.org/15d6af8b7c40f74797f6f68c7da9cda5b4b7ed6686111c53323ea6ceed285d3b", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/raim/actions/runs/38371030858" }, { "r": "4.6.1", "os": "mac", "version": "0.1.3", "date": "2026-10-13T08:52:00.000Z", "arch": "aarch64", "commit": "91505fd75333466c9568b66112b037a7cdd09b73", "fileid": "https://r2.ropensci.org/dab7dc94a31829fd017790449734502cb44e4b4b01ead5133308e19e8da1fc95", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/raim/actions/runs/38371030858" }, { "r": "4.6.1", "os": "mac", "version": "0.1.3", "date": "2026-10-13T08:51:16.000Z", "arch": "x86_64", "commit": "91505fd75333466c9568b66112b037a7cdd09b73", "fileid": "https://r2.ropensci.org/1e6a0bc3472869c4fc402df21576c7f80ecf4c63b8eb82ca8b25236529237a38", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/raim/actions/runs/38371030858" }, { "r": "4.6.0", "os": "wasm", "version": "0.1.3", "date": "2026-10-13T08:48:19.000Z", "arch": "emscripten", "commit": "91505fd75333466c9568b66112b037a7cdd09b73", "fileid": "https://r2.ropensci.org/fe4cab91dab0949121aca089a113b7c25f70f0232ad8e847471718adea24b9b7", "status": "success", "buildurl": "https://github.com/r-universe/raim/actions/runs/38371030858" }, { "r": "4.7.0", "os": "win", "version": "0.1.3", "date": "2026-10-13T08:49:11.000Z", "arch": "aarch64", "commit": "91505fd75333466c9568b66112b037a7cdd09b73", "fileid": "https://r2.ropensci.org/5526ade2da8121a4e472a80258961f4e45e7527800aaa508536982188d3d8ee7", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/raim/actions/runs/38371030858" }, { "r": "4.7.0", "os": "win", "version": "0.1.3", "date": "2026-10-13T08:47:24.000Z", "arch": "x86_64", "commit": "91505fd75333466c9568b66112b037a7cdd09b73", "fileid": "https://r2.ropensci.org/211fc52def22e5f727661ae3b90ef4b6caaca22b94912dabf8aa80f5536b083a", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/raim/actions/runs/38371030858" }, { "r": "4.5.3", "os": "win", "version": "0.1.3", "date": "2026-10-13T08:47:37.000Z", "arch": "x86_64", "commit": "91505fd75333466c9568b66112b037a7cdd09b73", "fileid": "https://r2.ropensci.org/cafae7c5f9487297ce54ffc06a79b072aed93e8c6ec33da8aee285d1243ebbd2", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/raim/actions/runs/38371030858" }, { "r": "4.6.1", "os": "win", "version": "0.1.3", "date": "2026-10-13T08:49:16.000Z", "arch": "aarch64", "commit": "91505fd75333466c9568b66112b037a7cdd09b73", "fileid": "https://r2.ropensci.org/1c7f52400bdf667f2527e6d01e3c3618c72e3b4fa567a37127e592bd2aaeed44", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/raim/actions/runs/38371030858" }, { "r": "4.6.1", "os": "win", "version": "0.1.3", "date": "2026-10-13T08:48:14.000Z", "arch": "x86_64", "commit": "91505fd75333466c9568b66112b037a7cdd09b73", "fileid": "https://r2.ropensci.org/eb7f599156e121589aa7b3219e4e03731a9da72482e4df209ada7e12bf634221", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/raim/actions/runs/38371030858" } ] }