{ "_id": "6a101f7eacfb0bcc41c8b3f2", "Package": "TemporalGSSA", "Type": "Package", "Title": "Outputs Temporal Profile of Molecules from Stochastic Simulation\nAlgorithm Generated Datasets", "Version": "1.0.1", "Author": "Siddhartha Kundu", "Maintainer": "Siddhartha Kundu ", "Description": "The data that is generated from independent and\nconsecutive 'GillespieSSA' runs for a generic biochemical\nnetwork is formatted as rows and constitutes an observation.\nThe first column of each row is the computed timestep for each\nrun. Subsequent columns are used for the number of molecules of\neach participating molecular species or \"metabolite\" of a\ngeneric biochemical network. In this way 'TemporalGSSA', is a\nwrapper for the R-package 'GillespieSSA'. The number of\nobservations must be at least 30. This will generate data that\nis statistically significant. 'TemporalGSSA', transforms this\nraw data into a simulation time-dependent and\nmetabolite-specific trial. Each such trial is defined as a set\nof linear models (n >= 30) between a timestep and number of\nmolecules for a metabolite. Each linear model is characterized\nby coefficients such as the slope, arbitrary constant, etc. The\nuser must enter an integer from 1-4. These specify the\nstatistical modality utilized to compute a representative\ntimestep (mean, median, random, all). These arguments are\nmandatory and will be checked. Whilst, the numeric indicator\n\"0\" indicates suitability, \"1\" prompts the user to revise and\nre-enter their data. An optional logical argument controls the\noutput to the console with the default being \"TRUE\" (curtailed)\nwhilst \"FALSE\" (verbose). The coefficients of each linear model\nare averaged (mean slope, mean constant) and are incorporated\ninto a metabolite-specific linear regression model as the\ndependent variable. The independent variable is the\nrepresentative timestep chosen previously. The generated data\nis the imputed molecule number for an in silico experiment with\n(n >=30) observations. These steps can be replicated with\nmultiple set of observations. The generated \"technical\nreplicates\" can be statistically evaluated (mean, standard\ndeviation) and will constitute simulation time-dependent\nmolecules for each metabolite. For SSA-generated datasets with\nvarying simulation times 'TemporalGSSA' will generate a\nsimulation time-dependent trajectory for each metabolite of the\nbiochemical network under study. The relevant publication with\nthe mathematical derivation of the algorithm is (2022, Journal\nof Bioinformatics and Computational Biology)\n. The algorithm has been\ndeployed in the following publications (2021, Heliyon)\n and (2016, Journal of\nTheoretical Biology) .", "License": "GPL-3", "Encoding": "UTF-8", "RoxygenNote": "7.1.2", "Config/testthat/edition": "3", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-14 06:45:07 UTC", "User": "root" }, "Repository": "https://cran.r-universe.dev", "Date/Publication": "2022-10-09 13:10:02 UTC", "RemoteUrl": "https://github.com/cran/TemporalGSSA", "RemoteRef": "HEAD", "RemoteSha": "58c9cedacb721d846064098a03f9f8b45a9e15f5", "MD5sum": "a371cc15714a4c8683c38fffdd75ed92", "_user": "cran", "_type": "src", "_file": "TemporalGSSA_1.0.1.tar.gz", "_fileid": "d466ca2b30355451d17e919a62172f60598ae1727e0c35fdfcba2e413532bdc8", "_filesize": 86602, "_sha256": "d466ca2b30355451d17e919a62172f60598ae1727e0c35fdfcba2e413532bdc8", "_created": "2026-05-14T06:45:07.000Z", "_published": "2026-05-22T09:18:54.103Z", "_distro": "noble", "_jobs": [ { "job": 77351363060, "time": 115, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "6988800776" }, { "job": 77351362724, "time": 99, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "6988796092" }, { "job": 77351361916, "time": 185, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "6988773782" }, { "job": 77351362051, "time": 85, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7157087375" } ], "_buildurl": "https://github.com/r-universe/cran/actions/runs/25846035396", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/TemporalGSSA", "_commit": { "id": "58c9cedacb721d846064098a03f9f8b45a9e15f5", "author": "Siddhartha Kundu ", "committer": "cran-robot ", "message": "version 1.0.1\n", "time": 1665321002 }, "_maintainer": { "name": "Siddhartha Kundu", "email": "siddhartha_kundu@aiims.edu" }, "_registered": true, "_dependencies": [ { "package": "stats", "role": "Depends" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "cran", "_selfowned": false, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 0, "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 195, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/TemporalGSSA" }, "_searchresults": 1, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/TemporalGSSA.html", "manual.pdf" ], "_realowner": "cran", "_cranurl": false, "_releases": [ { "version": "1.0.0", "date": "2022-03-02" }, { "version": "1.0.1", "date": "2022-10-09" } ], "_exports": [ "calculate_TemporalGSSA" ], "_help": [ { "page": "calculate_TemporalGSSA", "title": "calculate_TemporalGSSA() This is the main function of the package 'TemporalGSSA'.", "topics": [ "calculate_TemporalGSSA" ] }, { "page": "check_TemporalGSSA", "title": "check_TemporalGSSA()", "topics": [ "check_TemporalGSSA" ] } ], "_rundeps": [], "_score": 1, "_indexed": true, "_nocasepkg": "temporalgssa", "_universes": [ "cran" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.1", "date": "2026-05-14T06:47:18.000Z", "distro": "noble", "commit": "58c9cedacb721d846064098a03f9f8b45a9e15f5", "fileid": "4b30d86e899075b9f84e8d426a199d5b8959b311fb12febbce21c740887bf559", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/25846035396" }, { "r": "4.6.0", "os": "linux", "version": "1.0.1", "date": "2026-05-14T06:46:56.000Z", "distro": "noble", "commit": "58c9cedacb721d846064098a03f9f8b45a9e15f5", "fileid": "9c8bb0715c035ccb5aa0d91d070d739cf95497e215f81c23b6823b8e400b7e87", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/25846035396" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.1", "date": "2026-05-22T09:18:40.000Z", "commit": "58c9cedacb721d846064098a03f9f8b45a9e15f5", "fileid": "ee94e7a94f4ccdcee355a9a871feeacfc8760f256421b5ca2abcac3819b2dd22", "status": "success", "buildurl": "https://github.com/r-universe/cran/actions/runs/25846035396" } ] }