{"id":22092173,"url":"https://github.com/pcruniversum/chippcr","last_synced_at":"2025-07-24T20:32:04.461Z","repository":{"id":16528041,"uuid":"19281268","full_name":"PCRuniversum/chipPCR","owner":"PCRuniversum","description":"Toolkit of helper functions to pre-process amplification data","archived":false,"fork":false,"pushed_at":"2021-02-27T20:21:20.000Z","size":9513,"stargazers_count":8,"open_issues_count":4,"forks_count":7,"subscribers_count":4,"default_branch":"master","last_synced_at":"2024-11-28T22:41:38.450Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":"StrykerKKD/SpaceInvaders","license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/PCRuniversum.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG","contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2014-04-29T15:22:30.000Z","updated_at":"2024-02-09T21:23:34.000Z","dependencies_parsed_at":"2022-07-25T05:32:04.811Z","dependency_job_id":null,"html_url":"https://github.com/PCRuniversum/chipPCR","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PCRuniversum%2FchipPCR","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PCRuniversum%2FchipPCR/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PCRuniversum%2FchipPCR/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PCRuniversum%2FchipPCR/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/PCRuniversum","download_url":"https://codeload.github.com/PCRuniversum/chipPCR/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":227476144,"owners_count":17779417,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-12-01T03:08:36.452Z","updated_at":"2024-12-01T03:08:37.247Z","avatar_url":"https://github.com/PCRuniversum.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![published in: Bioinformatics](https://img.shields.io/badge/published%20in-Bioinformatics-ff69b4.svg?style=flat)](https://doi.org/10.1093/bioinformatics/btv205)\n[![R-CMD-check](https://github.com/PCRuniversum/chipPCR/workflows/R-CMD-check/badge.svg)](https://github.com/PCRuniversum/chipPCR/actions)\n\nThe chipPCR package is a toolkit of functions to preprocess \namplification curve data. Amplification data can be obtained from \nconventional PCR reactions or isothermal amplification reactions. The \npackage contains functions to normalize and baseline amplification curves, \na routine to detect the start of an amplification reaction, several \nsmoothers for amplification data, a function to distinguish positive and \nnegative amplification reactions and a function to determine the \namplification efficiency. The smoothers are based on LOWESS, moving \naverage, cubic splines, Savitzky-Golay and others.\n\nIn addition the first \napproximate approximate derivative maximum (FDM) and second approximate \nderivative maximum (SDM) can be calculated by a 5-point-stencil as \nquantification points from real-time amplification curves. chipPCR contains \ndata sets of experimental nucleic acid amplification systems including the \nVideoScan HCU and a capillary convective PCR (ccPCR) system. The \namplification data were generated by helicase dependent amplification (HDA) \nor polymerase chain reaction (PCR) under various temperature conditions. As \ndetection system intercalating dyes (EvaGreen, SYBR Green) and hydrolysis \nprobes (TaqMan) were used.\n\nInstallation\n------------\n\nchipPCR is available [on CRAN](https://CRAN.R-project.org/package=chipPCR), so installation is as simple as:\n\n```\ninstall.packages(\"chipPCR\")\n```\n\nYou can install the latest development version of the code directly from GitHub:\n\n```\nsource(\"https://install-github.me/michbur/chipPCR\")\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpcruniversum%2Fchippcr","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpcruniversum%2Fchippcr","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpcruniversum%2Fchippcr/lists"}