{ "_id": "6a104be7acfb0bcc41ca00cf", "Package": "PCRedux", "Type": "Package", "Title": "Quantitative Polymerase Chain Reaction (qPCR) Data Mining and\nMachine Learning Toolkit", "Version": "1.1-2", "Date": "2022-05-11", "Authors@R": "c(person(\"Stefan\", \"Roediger\", \nemail = \"stefan.roediger@b-tu.de\",\ncomment = c(ORCID = \"0000-0002-1441-6512\"),\nrole = c(\"cre\", \"aut\")),\nperson(\"Michal\", \"Burdukiewicz\",\nemail = \"michalburdukiewicz@gmail.com\",\ncomment = c(ORCID = \"0000-0001-8926-582X\"),\nrole = c(\"aut\")),\nperson(\"Andrej-Nikolai\", \"Spiess\",\nemail = \"a.spiess@uke.de\",\ncomment = c(ORCID = \"0000-0002-9630-4724\"),\nrole = c(\"aut\")),\nperson(\"Konstantin A.\", \"Blagodatskikh\",\nemail = \"k.blag@yandex.ru\",\ncomment = c(ORCID = \"0000-0002-8732-0300\"),\nrole = c(\"aut\")),\nperson(\"Dominik\", \"Rafacz\",\nemail = \"dominikrafacz@gmail.com\",\ncomment = c(ORCID = \"0000-0003-0925-1909\"),\nrole = c(\"ctb\")))", "Description": "Extracts features from amplification curve data of\nquantitative Polymerase Chain Reactions (qPCR) (Pabinger S. et\nal. (2014) ) for machine\nlearning purposes. Helper functions prepare the amplification\ncurve data for processing as functional data (e.g., Hausdorff\ndistance) or enable the plotting of amplification curve classes\n(negative, ambiguous, positive). The hookreg() and hookregNL()\nfunctions (Burdukiewicz M. et al. (2018)\n) can be used to predict\namplification curves with an hook effect-like curvature. The\npcrfit_single() function can be used to extract features from\nan amplification curve. PCRedux was published in the Journal of\nOpen Source Software (<10.21105/joss.04407>).", "License": "MIT + file LICENSE", "LazyLoad": "yes", "LazyData": "yes", "URL": "https://CRAN.R-project.org/package=PCRedux", "BugReports": "https://github.com/PCRuniversum/PCRedux/issues", "NeedsCompilation": "no", "VignetteBuilder": "knitr", "Encoding": "UTF-8", "Language": "en-US", "RoxygenNote": "7.3.2", "Config/pak/sysreqs": "cmake libfreetype6-dev libglu1-mesa-dev make\ntexlive libpng-dev libuv1-dev libgl1-mesa-dev zlib1g-dev", "Repository": "https://pcruniversum.r-universe.dev", "Date/Publication": "2024-07-28 15:11:13 UTC", "RemoteUrl": "https://github.com/pcruniversum/pcredux", "RemoteRef": "HEAD", "RemoteSha": "28ed591f181cb68ac3dd93da319010ff48078e4a", "Packaged": { "Date": "2026-05-10 07:48:44 UTC", "User": "root" }, "Author": "Stefan Roediger [cre, aut] (ORCID:\n),\nMichal Burdukiewicz [aut] (ORCID:\n),\nAndrej-Nikolai Spiess [aut] (ORCID:\n),\nKonstantin A. Blagodatskikh [aut] (ORCID:\n),\nDominik Rafacz [ctb] (ORCID: )", "Maintainer": "Stefan Roediger ", "MD5sum": "9ec08347d48123ec38fc37a5a0848e05", "_user": "pcruniversum", "_type": "src", "_file": "PCRedux_1.1-2.tar.gz", "_fileid": "3cfcb2500e24c73e43527208561f2e08d644fe28ec073aa076fd7ad39446a210", "_filesize": 2076582, "_sha256": "3cfcb2500e24c73e43527208561f2e08d644fe28ec073aa076fd7ad39446a210", "_created": "2026-05-10T07:48:44.000Z", "_published": "2026-05-22T12:28:23.512Z", "_distro": "noble", "_jobs": [ { "job": 77379098935, "time": 238, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "6902098110" }, { "job": 77379099196, "time": 230, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "6902097300" }, { "job": 77379099202, "time": 109, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "6902084764" }, { "job": 77379098781, "time": 141, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "6902088097" }, { "job": 77379098306, "time": 281, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "6902073645" }, { "job": 77379097996, "time": 196, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7160463926" }, { "job": 77379098727, "time": 150, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "6902089139" }, { "job": 77379099158, "time": 127, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "6902086616" }, { "job": 77379099040, "time": 127, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "6902086602" } ], "_buildurl": "https://github.com/r-universe/pcruniversum/actions/runs/25623209082", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/pcruniversum/pcredux", "_commit": { "id": "28ed591f181cb68ac3dd93da319010ff48078e4a", "author": "michbur ", "committer": "michbur ", "message": "switching off rgl\n", "time": 1722179473 }, "_maintainer": { "name": "Stefan Roediger", "email": "stefan.roediger@b-tu.de", "login": "devsjr", "uuid": 5408324, "orcid": "0000-0002-1441-6512" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "changepoint", "role": "Imports" }, { "package": "chipPCR", "role": "Imports" }, { "package": "ecp", "role": "Imports" }, { "package": "fda.usc", "role": "Imports" }, { "package": "MBmca", "role": "Imports" }, { "package": "pbapply", "role": "Imports" }, { "package": "pracma", "role": "Imports" }, { "package": "qpcR", "role": "Imports" }, { "package": "robustbase", "role": "Imports" }, { "package": "segmented", "role": "Imports" }, { "package": "shiny", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "zoo", "role": "Imports" }, { "package": "DT", "role": "Suggests" }, { "package": "future", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "listenv", "role": "Suggests" }, { "package": "RDML", "role": "Suggests" }, { "package": "readxl", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "shinycssloaders", "role": "Suggests" }, { "package": "spelling", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "xtable", "role": "Suggests" } ], "_owner": "pcruniversum", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 8, "_contributors": [ { "user": "devsjr", "count": 405, "uuid": 5408324 }, { "user": "michbur", "count": 137, "uuid": 5267317 }, { "user": "kablag", "count": 14, "uuid": 1788726 }, { "user": "dominikrafacz", "count": 3, "uuid": 32573752 }, { "user": "csoneson", "count": 2, "uuid": 5628952 }, { "user": "anspiess", "count": 2, "uuid": 13885812 } ], "_userbio": { "uuid": 57115945, "type": "organization", "name": "PCRuniversum" }, "_downloads": { "count": 276, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/PCRedux" }, "_mentions": 1, "_devurl": "https://github.com/pcruniversum/pcredux", "_searchresults": 56, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/PCRedux.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/pcruniversum/pcredux", "_realowner": "pcruniversum", "_cranurl": true, "_releases": [ { "version": "0.2.5-1", "date": "2017-11-20" }, { "version": "0.2.6", "date": "2018-05-14" }, { "version": "0.2.6-1", "date": "2018-06-13" }, { "version": "0.2.6-4", "date": "2018-10-28" }, { "version": "1.0-1", "date": "2019-10-29" }, { "version": "1.0-2", "date": "2019-10-31" }, { "version": "1.0-4", "date": "2020-01-08" }, { "version": "1.0-6", "date": "2020-03-06" }, { "version": "1.1", "date": "2021-03-16" }, { "version": "1.1-2", "date": "2022-05-11" }, { "version": "1.2-0", "date": "2025-06-13" }, { "version": "1.2-1", "date": "2025-11-19" } ], "_exports": [ "armor", "autocorrelation_test", "decision_modus", "earlyreg", "encu", "head2tailratio", "hookreg", "hookregNL", "humanrater2", "mblrr", "pcrfit_single", "performeR", "qPCR2fdata", "run_PCRedux", "tReem", "winklR" ], "_datasets": [ { "name": "data_sample", "title": "The datasets implemented in PCRedux", "object": "data_sample", "class": [ "data.frame" ], "fields": [ "dataset", "decision", "runs", "cpD1", "cpD2", "cpD2_approx", "cpD2_ratio", "eff", "sliwin", "cpDdiff", "loglin_slope", "cpD2_range", "top", "f.top", "tdp", "f.tdp", "bg.stop", "amp.stop", "b_slope", "b_model_param", "c_model_param", "d_model_param", "e_model_param", "f_model_param", "f_intercept", "convInfo_iteratons", "qPCRmodel", "qPCRmodelRF", "minRFU", "maxRFU", "init2", "fluo", "slope_bg", "intercept_bg", "sigma_bg", "sd_bg", "head2tail_ratio", "mblrr_slope_pt", "mblrr_intercept_bg", "mblrr_slope_bg", "mblrr_cor_bg", "mblrr_intercept_pt", "mblrr_cor_pt", "polyarea", "peaks_ratio", "autocorellation", "cp_e.agglo", "cp_bcp", "amptester_shapiro", "amptester_lrt", "amptester_rgt", "amptester_tht", "amptester_slt", "amptester_polygon", "amptester_slope.ratio", "hookreg_hook", "hookreg_hook_slope", "hookreg_hook_delta", "central_angle", "number_of_cycles", "detection_chemistry", "device" ], "rows": 3302, "table": true, "tojson": true }, { "name": "decision_res_kbqPCR", "title": "The datasets implemented in PCRedux", "object": "decision_res_kbqPCR", "class": [ "data.frame" ], "fields": [ "kbqPCR", "test.result.1", "test.result.2", "test.result.3", "test.result.4", "test.result.5", "test.result.6", "test.result.7", "conformity" ], "rows": 400, "table": true, "tojson": true }, { "name": "kbqPCR", "title": "The datasets implemented in PCRedux", "object": "kbqPCR", "class": [ "data.frame" ], "fields": [ "cyc", "A01_p949_unkn_B2m", "A01_p949_unkn_HA1_G", "A01_p949_unkn_HA2_C", "A01_p949_unkn_HER2_C", "A01_p949_unkn_UTA2_T", "A02_p949_unkn_B2m", "A02_p949_unkn_HA1_A", "A02_p949_unkn_HA2_T", "A02_p949_unkn_HER2_G", "A02_p949_unkn_UTA2_C", "A03_p949_unkn_ADIR_T", "A03_p949_unkn_B2m", "A03_p949_unkn_C19ORF_T", "A03_p949_unkn_CLYBL_G", "A03_p949_unkn_TRIM22_C", "A04_p949_unkn_ADIR_C", "A04_p949_unkn_B2m", "A04_p949_unkn_C19ORF_A", "A04_p949_unkn_CLYBL_T", "A04_p949_unkn_TRIM22_T", "A05_p949_unkn_B2m", "A05_p949_unkn_PRCP_T", "A05_p949_unkn_SSR1_A", "A05_p949_unkn_T4A1_C", "A05_p949_unkn_WNK1_G", "A06_p949_unkn_B2m", "A06_p949_unkn_PRCP_G", "A06_p949_unkn_SSR1_G", "A06_p949_unkn_T4A1_A", "A06_p949_unkn_WNK1_T", "A07_p949_unkn_B2m", "A07_p949_unkn_HA.8_C", "A07_p949_unkn_HIVE_A", "A07_p949_unkn_NISCH_C", "A07_p949_unkn_UGT2b17_.", "A08_p949_unkn_B2m", "A08_p949_unkn_HA.8_G", "A08_p949_unkn_HIVE_G", "A08_p949_unkn_NISCH_T", "A08_p949_unkn_UGT2b17_.", "A09_p949_unkn_B2m", "A09_p949_unkn_CCL4.1T_T", "A09_p949_unkn_NCAPD3.1Q_C", "A09_p949_unkn_NDC80.1P_G", "A09_p949_unkn_WDR27.1L_A", "A10_p949_unkn_B2m", "A10_p949_unkn_CCL4.1T_A", "A10_p949_unkn_NCAPD3.1Q_T", "A10_p949_unkn_NDC80.1P_C", "A10_p949_unkn_WDR27.1L_G", "B01_p950_unkn_B2m", "B01_p950_unkn_HA1_G", "B01_p950_unkn_HA2_C", "B01_p950_unkn_HER2_C", "B01_p950_unkn_UTA2_T", "B02_p950_unkn_B2m", "B02_p950_unkn_HA1_A", "B02_p950_unkn_HA2_T", "B02_p950_unkn_HER2_G", "B02_p950_unkn_UTA2_C", "B03_p950_unkn_ADIR_T", "B03_p950_unkn_B2m", "B03_p950_unkn_C19ORF_T", "B03_p950_unkn_CLYBL_G", "B03_p950_unkn_TRIM22_C", "B04_p950_unkn_ADIR_C", "B04_p950_unkn_B2m", "B04_p950_unkn_C19ORF_A", "B04_p950_unkn_CLYBL_T", "B04_p950_unkn_TRIM22_T", "B05_p950_unkn_B2m", "B05_p950_unkn_PRCP_T", "B05_p950_unkn_SSR1_A", "B05_p950_unkn_T4A1_C", "B05_p950_unkn_WNK1_G", "B06_p950_unkn_B2m", "B06_p950_unkn_PRCP_G", "B06_p950_unkn_SSR1_G", "B06_p950_unkn_T4A1_A", "B06_p950_unkn_WNK1_T", "B07_p950_unkn_B2m", "B07_p950_unkn_HA.8_C", "B07_p950_unkn_HIVE_A", "B07_p950_unkn_NISCH_C", "B07_p950_unkn_UGT2b17_.", "B08_p950_unkn_B2m", "B08_p950_unkn_HA.8_G", "B08_p950_unkn_HIVE_G", "B08_p950_unkn_NISCH_T", "B08_p950_unkn_UGT2b17_.", "B09_p950_unkn_B2m", "B09_p950_unkn_CCL4.1T_T", "B09_p950_unkn_NCAPD3.1Q_C", "B09_p950_unkn_NDC80.1P_G", "B09_p950_unkn_WDR27.1L_A", "B10_p950_unkn_B2m", "B10_p950_unkn_CCL4.1T_A", "B10_p950_unkn_NCAPD3.1Q_T", "B10_p950_unkn_NDC80.1P_C", "B10_p950_unkn_WDR27.1L_G", "C01_p951_unkn_B2m", "C01_p951_unkn_HA1_G", "C01_p951_unkn_HA2_C", "C01_p951_unkn_HER2_C", "C01_p951_unkn_UTA2_T", "C02_p951_unkn_B2m", "C02_p951_unkn_HA1_A", "C02_p951_unkn_HA2_T", "C02_p951_unkn_HER2_G", "C02_p951_unkn_UTA2_C", "C03_p951_unkn_ADIR_T", "C03_p951_unkn_B2m", "C03_p951_unkn_C19ORF_T", "C03_p951_unkn_CLYBL_G", "C03_p951_unkn_TRIM22_C", "C04_p951_unkn_ADIR_C", "C04_p951_unkn_B2m", "C04_p951_unkn_C19ORF_A", "C04_p951_unkn_CLYBL_T", "C04_p951_unkn_TRIM22_T", "C05_p951_unkn_B2m", "C05_p951_unkn_PRCP_T", "C05_p951_unkn_SSR1_A", "C05_p951_unkn_T4A1_C", "C05_p951_unkn_WNK1_G", "C06_p951_unkn_B2m", "C06_p951_unkn_PRCP_G", "C06_p951_unkn_SSR1_G", "C06_p951_unkn_T4A1_A", "C06_p951_unkn_WNK1_T", "C07_p951_unkn_B2m", "C07_p951_unkn_HA.8_C", "C07_p951_unkn_HIVE_A", "C07_p951_unkn_NISCH_C", "C07_p951_unkn_UGT2b17_.", "C08_p951_unkn_B2m", "C08_p951_unkn_HA.8_G", "C08_p951_unkn_HIVE_G", "C08_p951_unkn_NISCH_T", "C08_p951_unkn_UGT2b17_.", "C09_p951_unkn_B2m", "C09_p951_unkn_CCL4.1T_T", "C09_p951_unkn_NCAPD3.1Q_C", "C09_p951_unkn_NDC80.1P_G", "C09_p951_unkn_WDR27.1L_A", "C10_p951_unkn_B2m", "C10_p951_unkn_CCL4.1T_A", "C10_p951_unkn_NCAPD3.1Q_T", "C10_p951_unkn_NDC80.1P_C", "C10_p951_unkn_WDR27.1L_G", "D01_p953_unkn_B2m", "D01_p953_unkn_HA1_G", "D01_p953_unkn_HA2_C", "D01_p953_unkn_HER2_C", "D01_p953_unkn_UTA2_T", "D02_p953_unkn_B2m", "D02_p953_unkn_HA1_A", "D02_p953_unkn_HA2_T", "D02_p953_unkn_HER2_G", "D02_p953_unkn_UTA2_C", "D03_p953_unkn_ADIR_T", "D03_p953_unkn_B2m", "D03_p953_unkn_C19ORF_T", "D03_p953_unkn_CLYBL_G", "D03_p953_unkn_TRIM22_C", "D04_p953_unkn_ADIR_C", "D04_p953_unkn_B2m", "D04_p953_unkn_C19ORF_A", "D04_p953_unkn_CLYBL_T", "D04_p953_unkn_TRIM22_T", "D05_p953_unkn_B2m", "D05_p953_unkn_PRCP_T", "D05_p953_unkn_SSR1_A", "D05_p953_unkn_T4A1_C", "D05_p953_unkn_WNK1_G", "D06_p953_unkn_B2m", "D06_p953_unkn_PRCP_G", "D06_p953_unkn_SSR1_G", "D06_p953_unkn_T4A1_A", "D06_p953_unkn_WNK1_T", "D07_p953_unkn_B2m", "D07_p953_unkn_HA.8_C", "D07_p953_unkn_HIVE_A", "D07_p953_unkn_NISCH_C", "D07_p953_unkn_UGT2b17_.", "D08_p953_unkn_B2m", "D08_p953_unkn_HA.8_G", "D08_p953_unkn_HIVE_G", "D08_p953_unkn_NISCH_T", "D08_p953_unkn_UGT2b17_.", "D09_p953_unkn_B2m", "D09_p953_unkn_CCL4.1T_T", "D09_p953_unkn_NCAPD3.1Q_C", "D09_p953_unkn_NDC80.1P_G", "D09_p953_unkn_WDR27.1L_A", "D10_p953_unkn_B2m", "D10_p953_unkn_CCL4.1T_A", "D10_p953_unkn_NCAPD3.1Q_T", "D10_p953_unkn_NDC80.1P_C", "D10_p953_unkn_WDR27.1L_G", "E01_p954_unkn_B2m", "E01_p954_unkn_HA1_G", "E01_p954_unkn_HA2_C", "E01_p954_unkn_HER2_C", "E01_p954_unkn_UTA2_T", "E02_p954_unkn_B2m", "E02_p954_unkn_HA1_A", "E02_p954_unkn_HA2_T", "E02_p954_unkn_HER2_G", "E02_p954_unkn_UTA2_C", "E03_p954_unkn_ADIR_T", "E03_p954_unkn_B2m", "E03_p954_unkn_C19ORF_T", "E03_p954_unkn_CLYBL_G", "E03_p954_unkn_TRIM22_C", "E04_p954_unkn_ADIR_C", "E04_p954_unkn_B2m", "E04_p954_unkn_C19ORF_A", "E04_p954_unkn_CLYBL_T", "E04_p954_unkn_TRIM22_T", "E05_p954_unkn_B2m", "E05_p954_unkn_PRCP_T", "E05_p954_unkn_SSR1_A", "E05_p954_unkn_T4A1_C", "E05_p954_unkn_WNK1_G", "E06_p954_unkn_B2m", "E06_p954_unkn_PRCP_G", "E06_p954_unkn_SSR1_G", "E06_p954_unkn_T4A1_A", "E06_p954_unkn_WNK1_T", "E07_p954_unkn_B2m", "E07_p954_unkn_HA.8_C", "E07_p954_unkn_HIVE_A", "E07_p954_unkn_NISCH_C", "E07_p954_unkn_UGT2b17_.", "E08_p954_unkn_B2m", "E08_p954_unkn_HA.8_G", "E08_p954_unkn_HIVE_G", "E08_p954_unkn_NISCH_T", "E08_p954_unkn_UGT2b17_.", "E09_p954_unkn_B2m", "E09_p954_unkn_CCL4.1T_T", "E09_p954_unkn_NCAPD3.1Q_C", "E09_p954_unkn_NDC80.1P_G", "E09_p954_unkn_WDR27.1L_A", "E10_p954_unkn_B2m", "E10_p954_unkn_CCL4.1T_A", "E10_p954_unkn_NCAPD3.1Q_T", "E10_p954_unkn_NDC80.1P_C", "E10_p954_unkn_WDR27.1L_G", "F01_p955_unkn_B2m", "F01_p955_unkn_HA1_G", "F01_p955_unkn_HA2_C", "F01_p955_unkn_HER2_C", "F01_p955_unkn_UTA2_T", "F02_p955_unkn_B2m", "F02_p955_unkn_HA1_A", "F02_p955_unkn_HA2_T", "F02_p955_unkn_HER2_G", "F02_p955_unkn_UTA2_C", "F03_p955_unkn_ADIR_T", "F03_p955_unkn_B2m", "F03_p955_unkn_C19ORF_T", "F03_p955_unkn_CLYBL_G", "F03_p955_unkn_TRIM22_C", "F04_p955_unkn_ADIR_C", "F04_p955_unkn_B2m", "F04_p955_unkn_C19ORF_A", "F04_p955_unkn_CLYBL_T", "F04_p955_unkn_TRIM22_T", "F05_p955_unkn_B2m", "F05_p955_unkn_PRCP_T", "F05_p955_unkn_SSR1_A", "F05_p955_unkn_T4A1_C", "F05_p955_unkn_WNK1_G", "F06_p955_unkn_B2m", "F06_p955_unkn_PRCP_G", "F06_p955_unkn_SSR1_G", "F06_p955_unkn_T4A1_A", "F06_p955_unkn_WNK1_T", "F07_p955_unkn_B2m", "F07_p955_unkn_HA.8_C", "F07_p955_unkn_HIVE_A", "F07_p955_unkn_NISCH_C", "F07_p955_unkn_UGT2b17_.", "F08_p955_unkn_B2m", "F08_p955_unkn_HA.8_G", "F08_p955_unkn_HIVE_G", "F08_p955_unkn_NISCH_T", "F08_p955_unkn_UGT2b17_.", "F09_p955_unkn_B2m", "F09_p955_unkn_CCL4.1T_T", "F09_p955_unkn_NCAPD3.1Q_C", "F09_p955_unkn_NDC80.1P_G", "F09_p955_unkn_WDR27.1L_A", "F10_p955_unkn_B2m", "F10_p955_unkn_CCL4.1T_A", "F10_p955_unkn_NCAPD3.1Q_T", "F10_p955_unkn_NDC80.1P_C", "F10_p955_unkn_WDR27.1L_G", "G01_p956_unkn_B2m", "G01_p956_unkn_HA1_G", "G01_p956_unkn_HA2_C", "G01_p956_unkn_HER2_C", "G01_p956_unkn_UTA2_T", "G02_p956_unkn_B2m", "G02_p956_unkn_HA1_A", "G02_p956_unkn_HA2_T", "G02_p956_unkn_HER2_G", "G02_p956_unkn_UTA2_C", "G03_p956_unkn_ADIR_T", "G03_p956_unkn_B2m", "G03_p956_unkn_C19ORF_T", "G03_p956_unkn_CLYBL_G", "G03_p956_unkn_TRIM22_C", "G04_p956_unkn_ADIR_C", "G04_p956_unkn_B2m", "G04_p956_unkn_C19ORF_A", "G04_p956_unkn_CLYBL_T", "G04_p956_unkn_TRIM22_T", "G05_p956_unkn_B2m", "G05_p956_unkn_PRCP_T", "G05_p956_unkn_SSR1_A", "G05_p956_unkn_T4A1_C", "G05_p956_unkn_WNK1_G", "G06_p956_unkn_B2m", "G06_p956_unkn_PRCP_G", "G06_p956_unkn_SSR1_G", "G06_p956_unkn_T4A1_A", "G06_p956_unkn_WNK1_T", "G07_p956_unkn_B2m", "G07_p956_unkn_HA.8_C", "G07_p956_unkn_HIVE_A", "G07_p956_unkn_NISCH_C", "G07_p956_unkn_UGT2b17_.", "G08_p956_unkn_B2m", "G08_p956_unkn_HA.8_G", "G08_p956_unkn_HIVE_G", "G08_p956_unkn_NISCH_T", "G08_p956_unkn_UGT2b17_.", "G09_p956_unkn_B2m", "G09_p956_unkn_CCL4.1T_T", "G09_p956_unkn_NCAPD3.1Q_C", "G09_p956_unkn_NDC80.1P_G", "G09_p956_unkn_WDR27.1L_A", "G10_p956_unkn_B2m", "G10_p956_unkn_CCL4.1T_A", "G10_p956_unkn_NCAPD3.1Q_T", "G10_p956_unkn_NDC80.1P_C", "G10_p956_unkn_WDR27.1L_G", "H01_p957_unkn_B2m", "H01_p957_unkn_HA1_G", "H01_p957_unkn_HA2_C", "H01_p957_unkn_HER2_C", "H01_p957_unkn_UTA2_T", "H02_p957_unkn_B2m", "H02_p957_unkn_HA1_A", "H02_p957_unkn_HA2_T", "H02_p957_unkn_HER2_G", "H02_p957_unkn_UTA2_C", "H03_p957_unkn_ADIR_T", "H03_p957_unkn_B2m", "H03_p957_unkn_C19ORF_T", "H03_p957_unkn_CLYBL_G", "H03_p957_unkn_TRIM22_C", "H04_p957_unkn_ADIR_C", "H04_p957_unkn_B2m", "H04_p957_unkn_C19ORF_A", "H04_p957_unkn_CLYBL_T", "H04_p957_unkn_TRIM22_T", "H05_p957_unkn_B2m", "H05_p957_unkn_PRCP_T", "H05_p957_unkn_SSR1_A", "H05_p957_unkn_T4A1_C", "H05_p957_unkn_WNK1_G", "H06_p957_unkn_B2m", "H06_p957_unkn_PRCP_G", "H06_p957_unkn_SSR1_G", "H06_p957_unkn_T4A1_A", "H06_p957_unkn_WNK1_T", "H07_p957_unkn_B2m", "H07_p957_unkn_HA.8_C", "H07_p957_unkn_HIVE_A", "H07_p957_unkn_NISCH_C", "H07_p957_unkn_UGT2b17_.", "H08_p957_unkn_B2m", "H08_p957_unkn_HA.8_G", "H08_p957_unkn_HIVE_G", "H08_p957_unkn_NISCH_T", "H08_p957_unkn_UGT2b17_.", "H09_p957_unkn_B2m", "H09_p957_unkn_CCL4.1T_T", "H09_p957_unkn_NCAPD3.1Q_C", "H09_p957_unkn_NDC80.1P_G", "H09_p957_unkn_WDR27.1L_A", "H10_p957_unkn_B2m", "H10_p957_unkn_CCL4.1T_A", "H10_p957_unkn_NCAPD3.1Q_T", "H10_p957_unkn_NDC80.1P_C", "H10_p957_unkn_WDR27.1L_G" ], "rows": 40, "table": true, "tojson": true }, { "name": "RAS002", "title": "The datasets implemented in PCRedux", "object": "RAS002", "class": [ "data.frame" ], "fields": [ "cyc", "A01_gDNA.._unkn_B.Globin", "A01_gDNA.._unkn_HPRT1", "A02_gDNA.._unkn_B.Globin", "A02_gDNA.._unkn_HPRT1", "A03_gDNA.._unkn_B.Globin", "A03_gDNA.._unkn_HPRT1", "A04_gDNA.._unkn_B.Globin", "A04_gDNA.._unkn_HPRT1", "A05_gDNA.._unkn_B.Globin", "A05_gDNA.._unkn_HPRT1", "A06_gDNA.._unkn_B.Globin", "A06_gDNA.._unkn_HPRT1", "A07_gDNA.._unkn_B.Globin", "A07_gDNA.._unkn_HPRT1", "A08_gDNA.._unkn_B.Globin", "A08_gDNA.._unkn_HPRT1", "A09_gDNA.._unkn_B.Globin", "A09_gDNA.._unkn_HPRT1", "A10_gDNA.._unkn_B.Globin", "A10_gDNA.._unkn_HPRT1", "A11_gDNA.._unkn_B.Globin", "A11_gDNA.._unkn_HPRT1", "A12_gDNA.._unkn_B.Globin", "A12_gDNA.._unkn_HPRT1", "B01_gDNA.._unkn_B.Globin", "B01_gDNA.._unkn_HPRT1", "B02_gDNA.._unkn_B.Globin", "B02_gDNA.._unkn_HPRT1", "B03_gDNA.._unkn_B.Globin", "B03_gDNA.._unkn_HPRT1", "B04_gDNA.._unkn_B.Globin", "B04_gDNA.._unkn_HPRT1", "B05_gDNA.._unkn_B.Globin", "B05_gDNA.._unkn_HPRT1", "B06_gDNA.._unkn_B.Globin", "B06_gDNA.._unkn_HPRT1", "B07_gDNA.._unkn_B.Globin", "B07_gDNA.._unkn_HPRT1", "B08_gDNA.._unkn_B.Globin", "B08_gDNA.._unkn_HPRT1", "B09_gDNA.._unkn_B.Globin", "B09_gDNA.._unkn_HPRT1", "B10_gDNA.._unkn_B.Globin", "B10_gDNA.._unkn_HPRT1", "B11_gDNA.._unkn_B.Globin", "B11_gDNA.._unkn_HPRT1", "B12_gDNA.._unkn_B.Globin", "B12_gDNA.._unkn_HPRT1", "C01_gDNA.._unkn_B.Globin", "C01_gDNA.._unkn_HPRT1", "C02_gDNA.._unkn_B.Globin", "C02_gDNA.._unkn_HPRT1", "C03_gDNA.._unkn_B.Globin", "C03_gDNA.._unkn_HPRT1", "C04_gDNA.._unkn_B.Globin", "C04_gDNA.._unkn_HPRT1", "C05_gDNA.._unkn_B.Globin", "C05_gDNA.._unkn_HPRT1", "C06_gDNA.._unkn_B.Globin", "C06_gDNA.._unkn_HPRT1", "C07_gDNA.._unkn_B.Globin", "C07_gDNA.._unkn_HPRT1", "C08_gDNA.._unkn_B.Globin", "C08_gDNA.._unkn_HPRT1", "C09_gDNA.._unkn_B.Globin", "C09_gDNA.._unkn_HPRT1", "C10_gDNA.._unkn_B.Globin", "C10_gDNA.._unkn_HPRT1", "C11_gDNA.._unkn_B.Globin", "C11_gDNA.._unkn_HPRT1", "C12_gDNA.._unkn_B.Globin", "C12_gDNA.._unkn_HPRT1", "D01_gDNA.._unkn_B.Globin", "D01_gDNA.._unkn_HPRT1", "D02_gDNA.._unkn_B.Globin", "D02_gDNA.._unkn_HPRT1", "D03_gDNA.._unkn_B.Globin", "D03_gDNA.._unkn_HPRT1", "D04_gDNA.._unkn_B.Globin", "D04_gDNA.._unkn_HPRT1", "D05_gDNA.._unkn_B.Globin", "D05_gDNA.._unkn_HPRT1", "D06_gDNA.._unkn_B.Globin", "D06_gDNA.._unkn_HPRT1", "D07_gDNA.._unkn_B.Globin", "D07_gDNA.._unkn_HPRT1", "D08_gDNA.._unkn_B.Globin", "D08_gDNA.._unkn_HPRT1", "D09_gDNA.._unkn_B.Globin", "D09_gDNA.._unkn_HPRT1", "D10_gDNA.._unkn_B.Globin", "D10_gDNA.._unkn_HPRT1", "D11_gDNA.._unkn_B.Globin", "D11_gDNA.._unkn_HPRT1", "D12_gDNA.._unkn_B.Globin", "D12_gDNA.._unkn_HPRT1", "E01_gDNA.._unkn_B.Globin", "E01_gDNA.._unkn_HPRT1", "E02_gDNA.._unkn_B.Globin", "E02_gDNA.._unkn_HPRT1", "E03_gDNA.._unkn_B.Globin", "E03_gDNA.._unkn_HPRT1", "E04_gDNA.._unkn_B.Globin", "E04_gDNA.._unkn_HPRT1", "E05_gDNA.._unkn_B.Globin", "E05_gDNA.._unkn_HPRT1", "E06_gDNA.._unkn_B.Globin", "E06_gDNA.._unkn_HPRT1", "E07_gDNA.._unkn_B.Globin", "E07_gDNA.._unkn_HPRT1", "E08_gDNA.._unkn_B.Globin", "E08_gDNA.._unkn_HPRT1", "E09_gDNA.._unkn_B.Globin", "E09_gDNA.._unkn_HPRT1", "E10_gDNA.._unkn_B.Globin", "E10_gDNA.._unkn_HPRT1", "E11_gDNA.._unkn_B.Globin", "E11_gDNA.._unkn_HPRT1", "E12_gDNA.._unkn_B.Globin", "E12_gDNA.._unkn_HPRT1", "F01_gDNA.._unkn_B.Globin", "F01_gDNA.._unkn_HPRT1", "F02_gDNA.._unkn_B.Globin", "F02_gDNA.._unkn_HPRT1", "F03_gDNA.._unkn_B.Globin", "F03_gDNA.._unkn_HPRT1", "F04_gDNA.._unkn_B.Globin", "F04_gDNA.._unkn_HPRT1", "F05_gDNA.._unkn_B.Globin", "F05_gDNA.._unkn_HPRT1", "F06_gDNA.._unkn_B.Globin", "F06_gDNA.._unkn_HPRT1", "F07_gDNA.._unkn_B.Globin", "F07_gDNA.._unkn_HPRT1", "F08_gDNA.._unkn_B.Globin", "F08_gDNA.._unkn_HPRT1", "F09_gDNA.._unkn_B.Globin", "F09_gDNA.._unkn_HPRT1", "F10_gDNA.._unkn_B.Globin", "F10_gDNA.._unkn_HPRT1", "F11_gDNA.._unkn_B.Globin", "F11_gDNA.._unkn_HPRT1", "F12_gDNA.._unkn_B.Globin", "F12_gDNA.._unkn_HPRT1", "G01_gDNA.._unkn_B.Globin", "G01_gDNA.._unkn_HPRT1", "G02_gDNA.._unkn_B.Globin", "G02_gDNA.._unkn_HPRT1", "G03_gDNA.._unkn_B.Globin", "G03_gDNA.._unkn_HPRT1", "G04_gDNA.._unkn_B.Globin", "G04_gDNA.._unkn_HPRT1", "G05_gDNA.._unkn_B.Globin", "G05_gDNA.._unkn_HPRT1", "G06_gDNA.._unkn_B.Globin", "G06_gDNA.._unkn_HPRT1", "G07_gDNA.._unkn_B.Globin", "G07_gDNA.._unkn_HPRT1", "G08_gDNA.._unkn_B.Globin", "G08_gDNA.._unkn_HPRT1", "G09_gDNA.._unkn_B.Globin", "G09_gDNA.._unkn_HPRT1", "G10_gDNA.._unkn_B.Globin", "G10_gDNA.._unkn_HPRT1", "G11_gDNA.._unkn_B.Globin", "G11_gDNA.._unkn_HPRT1", "G12_gDNA.._unkn_B.Globin", "G12_gDNA.._unkn_HPRT1", "H01_ntc_ntc_B.Globin", "H01_ntc_ntc_HPRT1", "H02_ntc_ntc_B.Globin", "H02_ntc_ntc_HPRT1", "H03_ntc_ntc_B.Globin", "H03_ntc_ntc_HPRT1", "H04_ntc_ntc_B.Globin", "H04_ntc_ntc_HPRT1", "H05_ntc_ntc_B.Globin", "H05_ntc_ntc_HPRT1", "H06_ntc_ntc_B.Globin", "H06_ntc_ntc_HPRT1", "H07_ntc_ntc_B.Globin", "H07_ntc_ntc_HPRT1", "H08_ntc_ntc_B.Globin", "H08_ntc_ntc_HPRT1", "H09_ntc_ntc_B.Globin", "H09_ntc_ntc_HPRT1", "H10_ntc_ntc_B.Globin", "H10_ntc_ntc_HPRT1", "H11_ntc_ntc_B.Globin", "H11_ntc_ntc_HPRT1", "H12_ntc_ntc_B.Globin", "H12_ntc_ntc_HPRT1" ], "rows": 40, "table": true, "tojson": true }, { "name": "RAS002_decisions", "title": "The datasets implemented in PCRedux", "object": "RAS002_decisions", "class": [ "factor" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "armor", "title": "armor: fetch errors gently", "topics": [ "armor" ] }, { "page": "autocorrelation_test", "title": "A function to test for autocorrelation of amplification curve data from a quantitative PCR experiment", "topics": [ "autocorrelation_test" ] }, { "page": "decision_modus", "title": "A function to get a decision (modus) from a vector of classes", "topics": [ "decision_modus" ] }, { "page": "earlyreg", "title": "A function to calculate the slope and intercept of an amplification curve data from a quantitative PCR experiment.", "topics": [ "earlyreg" ] }, { "page": "encu", "title": "A function to calculate numerous features from amplification curve data from a quantitative PCR experiment.", "topics": [ "encu" ] }, { "page": "head2tailratio", "title": "A function to calculate to head to tail ratio of amplification curve data from a quantitative PCR experiment", "topics": [ "head2tailratio" ] }, { "page": "hookreg", "title": "A function to calculate the slope and intercept of an amplification curve data from a quantitative PCR experiment at the end of the data stream.", "topics": [ "hookreg" ] }, { "page": "hookregNL", "title": "hookregNL - A function to calculate the slope of amplification curves in the tail region", "topics": [ "hookregNL" ] }, { "page": "humanrater2", "title": "Human Rater 2.0", "topics": [ "humanrater2" ] }, { "page": "mblrr", "title": "A function to perform a Local Robust Regression in Ranges defined by Qunantile-filtering", "topics": [ "mblrr" ] }, { "page": "PCRedux", "title": "PCRedux - quantitative PCR Data Mining and Machine Learning Toolkit", "topics": [ "PCRedux-package", "PCRedux" ] }, { "page": "PCRedux_datasets", "title": "The datasets implemented in PCRedux", "topics": [ "data_sample", "decision_res_kbqPCR", "kbqPCR", "RAS002", "RAS002_decisions" ] }, { "page": "pcrfit_single", "title": "pcrfit_single - A function to extract features from an amplification curve", "topics": [ "pcrfit_single" ] }, { "page": "performeR", "title": "Performance analysis for binary classification", "topics": [ "performeR" ] }, { "page": "qPCR2fdata", "title": "A helper function to convert amplification curve data to the fdata format.", "topics": [ "qPCR2fdata" ] }, { "page": "run_PCRedux", "title": "PCRedux app", "topics": [ "run_PCRedux" ] }, { "page": "tReem", "title": "A function to Group Amplification Curves According to their Shape", "topics": [ "tReem" ] }, { "page": "winklR", "title": "winklR: A function to calculate the angle based on the first and the second derivative of an amplification curve data from a quantitative PCR experiment.", "topics": [ "winklR" ] } ], "_readme": "https://github.com/pcruniversum/pcredux/raw/HEAD/README.md", "_rundeps": [ "ash", "base64enc", "bitops", "bslib", "cachem", "changepoint", "chipPCR", "cli", "cluster", "codetools", "colorspace", "commonmark", "cpp11", "DEoptimR", "deSolve", "digest", "doParallel", "ecp", "evaluate", "farver", "fastmap", "fda", "fda.usc", "fds", "FNN", "fontawesome", "foreach", "fs", "ggplot2", "glue", "gtable", "hdrcde", "highr", "htmltools", "htmlwidgets", "httpuv", "isoband", "iterators", "jquerylib", "jsonlite", "kernlab", "KernSmooth", "knitr", "ks", "kSamples", "labeling", "later", "lattice", "lifecycle", "lmtest", "locfit", "magrittr", "MASS", "Matrix", "MatrixModels", "MBmca", "mclust", "memoise", "mgcv", "mime", "minpack.lm", "multicool", "mvtnorm", "nlme", "otel", "outliers", "pbapply", "pcaPP", "pracma", "promises", "ptw", "qpcR", "quantreg", "R6", "rainbow", "rappdirs", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppDE", "RCurl", "Rfit", "rgl", "rlang", "rmarkdown", "robustbase", "S7", "sass", "scales", "segmented", "shiny", "signal", "sourcetools", "SparseM", "SuppDists", "survival", "tinytex", "vctrs", "viridisLite", "withr", "xfun", "xtable", "yaml", "zoo" ], "_vignettes": [ { "source": "PCRedux.Rmd", "filename": "PCRedux.html", "title": "PCRedux package - an overview", "author": "The PCRedux package authors", "engine": "knitr::rmarkdown", "headings": [], "created": "2017-08-23 10:50:23", "modified": "2024-07-26 11:54:32", "commits": 144 } ], "_score": 6.049218022670182, "_indexed": true, "_nocasepkg": "pcredux", "_universes": [ "pcruniversum", "devsjr" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.1-2", "date": "2026-05-10T07:52:06.000Z", "distro": "noble", "commit": "28ed591f181cb68ac3dd93da319010ff48078e4a", "fileid": "f5b049c276d414668e7cb0685f90255da04cc5622a3feed7e036b57580451b7a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/pcruniversum/actions/runs/25623209082" }, { "r": "4.6.0", "os": "linux", "version": "1.1-2", "date": "2026-05-10T07:52:03.000Z", "distro": "noble", "commit": "28ed591f181cb68ac3dd93da319010ff48078e4a", "fileid": "a4c485c2be8200a81817efd304a36044f0d2524c79046d616e763b62eb805ea5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/pcruniversum/actions/runs/25623209082" }, { "r": "4.5.3", "os": "mac", "version": "1.1-2", "date": "2026-05-10T07:50:23.000Z", "commit": "28ed591f181cb68ac3dd93da319010ff48078e4a", "fileid": "e634cda5b2f7f68fef41d0e2d6960f4596eed1d6e43f9c847d6d791f454348f5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/pcruniversum/actions/runs/25623209082" }, { "r": "4.6.0", "os": "mac", "version": "1.1-2", "date": "2026-05-10T07:50:32.000Z", "commit": "28ed591f181cb68ac3dd93da319010ff48078e4a", "fileid": "77a33aba0e1eb0b6bcd0fe95078d53bc3792b2cc5ce4aa9d12b9726cd168a1e7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/pcruniversum/actions/runs/25623209082" }, { "r": "4.7.0", "os": "win", "version": "1.1-2", "date": "2026-05-10T07:50:29.000Z", "commit": "28ed591f181cb68ac3dd93da319010ff48078e4a", "fileid": "d41cf4ec284670810f8835e213c8f0825ed7e5525d43da1176df8b1404758762", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/pcruniversum/actions/runs/25623209082" }, { "r": "4.5.3", "os": "win", "version": "1.1-2", "date": "2026-05-10T07:50:14.000Z", "commit": "28ed591f181cb68ac3dd93da319010ff48078e4a", "fileid": "aa9cf6f7721a03847962657d8bc22e84dcbbf8ebd965dfb48aa44c298091248c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/pcruniversum/actions/runs/25623209082" }, { "r": "4.6.0", "os": "win", "version": "1.1-2", "date": "2026-05-10T07:50:08.000Z", "commit": "28ed591f181cb68ac3dd93da319010ff48078e4a", "fileid": "a3c2be293889169bf7bf460a48d54c7665735a61a4d328004db0871fe2e86aa2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/pcruniversum/actions/runs/25623209082" }, { "r": "4.6.0", "os": "wasm", "version": "1.1-2", "date": "2026-05-22T12:28:01.000Z", "commit": "28ed591f181cb68ac3dd93da319010ff48078e4a", "fileid": "56e1a96926bce88d14e7e866803a6417a35fbbb42b3ff2f1f4494e42d099e433", "status": "success", "buildurl": "https://github.com/r-universe/pcruniversum/actions/runs/25623209082" } ] }