{"id":35210885,"url":"https://github.com/kaizadp/nmrrr-workflow","last_synced_at":"2026-05-19T11:42:04.376Z","repository":{"id":53678540,"uuid":"237559838","full_name":"kaizadp/nmrrr-workflow","owner":"kaizadp","description":"general processing script for soil NMR data","archived":false,"fork":false,"pushed_at":"2023-03-28T21:24:41.000Z","size":45587,"stargazers_count":2,"open_issues_count":1,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-03-24T01:47:40.858Z","etag":null,"topics":["nmr","soil","spectra","template"],"latest_commit_sha":null,"homepage":"","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/kaizadp.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2020-02-01T04:09:44.000Z","updated_at":"2023-10-22T09:35:47.000Z","dependencies_parsed_at":"2022-09-19T00:00:37.220Z","dependency_job_id":null,"html_url":"https://github.com/kaizadp/nmrrr-workflow","commit_stats":{"total_commits":131,"total_committers":6,"mean_commits":"21.833333333333332","dds":0.5648854961832062,"last_synced_commit":"48372b47fa07a17fba184af7cdd54da21f681847"},"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/kaizadp/nmrrr-workflow","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kaizadp%2Fnmrrr-workflow","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kaizadp%2Fnmrrr-workflow/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kaizadp%2Fnmrrr-workflow/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kaizadp%2Fnmrrr-workflow/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/kaizadp","download_url":"https://codeload.github.com/kaizadp/nmrrr-workflow/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kaizadp%2Fnmrrr-workflow/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28119505,"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","status":"online","status_checked_at":"2025-12-29T02:00:07.021Z","response_time":58,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"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":["nmr","soil","spectra","template"],"created_at":"2025-12-29T18:02:52.921Z","updated_at":"2025-12-29T18:03:41.014Z","avatar_url":"https://github.com/kaizadp.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"\n\u003cimg align=\"right\" heignt = \"250\" width = \"250\" src=\"images/nmr_hex.png\"\u003e\n\n# nmrrr\n\nThis script is designed for batch processing and analysis of **NMR\nr**esults in **R** (nmrrr).\n\nUse this script for:  \n(a) plotting spectra  \n(b) calculating relative abundance of functional groups  \n(c) peak assignments\n\nBefore using this script, NMR spectra must be processed in MestreNova\n(phase corrected, baseline corrected, deconvoluted, peak picked,\nnormalized).\n\n------------------------------------------------------------------------\n\n2021-06-09 update: We are currently streamlining this workflow by\nconverting the script into reproducible functions. They can be found in\n`code/nmrrr_workflow/`. -KFP\n\n2021-07-10 update: The `vignettes` directory contains tutorials on how\nto use this package. The .md files are the rendered Markdown reports,\nand the .Rmd files are the source files for the reports. - KFP\n\n------------------------------------------------------------------------\n\nExample spectra:  \nspectra processed in MestreNova, with automated Global Spectral\nDeconvolution.  \nWater peak removed during processing. Avoid using DMSO and water regions\nfor further analyses.\n\n### spectra plot version 1: with banded regions for bins\n\nThis is good for visualization, not necessarily ideal for manuscripts.\n\n![gg\\_nmr1](images/spectra_1.png)\n\n### spectra plot version 2: with bracketed regions for bins\n\nPreferred for manuscripts.\n\n![gg\\_nmr2](images/spectra_2.png)\n\nThese bins were obtained from [Mitchell et al. 2018, *Soil\nSystems*](https://doi.org/10.3390/soils2010008).  \n(1) aliphatic polymethylene and methyl groups (0.6-1.3 ppm); (2) N- and\nO-substituted aliphatic (1.3–2.9 ppm); (3) O-alkyl (2.9–4.1 ppm); (4)\nα-proton of peptides (4.1–4.8 ppm); (5) anomeric proton of carbohydrates\n(4.8–5.2 ppm); (6) aromatic and phenolic (6.2–7.8 ppm); and (7) amide\n(7.8–8.4 ppm). The peak at 2.50 ppm arises from the solvent (DMSO-d6).\n\n------------------------------------------------------------------------\n\n## BINS USED\n\nThese are the options available in the file `0-NMR_BINS.csv`\n\n| binset name  | state    | solvent | reference                                                                           |\n|--------------|----------|---------|-------------------------------------------------------------------------------------|\n| Clemente2012 | solution | DMSO-d6 | [Clemente et al. *Environmental Chemistry*](https://doi.org/10.1071/EN11096)        |\n| Mitchell2018 | solution | DMSO-d6 | [Mitchell et al. 2018, *Soil Systems*](https://doi.org/10.3390/soils2010008)        |\n| Lynch2019    | solution | D2O     | [Lynch et al. *Global Biogeochemical Cycles*](https://doi.org/10.1029/2018GB006030) |\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkaizadp%2Fnmrrr-workflow","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fkaizadp%2Fnmrrr-workflow","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkaizadp%2Fnmrrr-workflow/lists"}