{"id":19705920,"url":"https://github.com/llnl/2022_dvrfs_microbiome","last_synced_at":"2026-06-12T11:31:31.782Z","repository":{"id":66082864,"uuid":"387202862","full_name":"LLNL/2022_DVRFS_microbiome","owner":"LLNL","description":"Scripts for a manuscript titled \"Subsurface Microbial Communities Reflect Regional-Scale Groundwater Hydraulic Connectivity\" (submitted)","archived":false,"fork":false,"pushed_at":"2022-07-10T18:26:22.000Z","size":63,"stargazers_count":0,"open_issues_count":0,"forks_count":2,"subscribers_count":4,"default_branch":"main","last_synced_at":"2025-01-10T12:23:46.858Z","etag":null,"topics":["groundwater","groundwater-flow","hydraulic-connectivity","microbial-communities","microbial-community-assembly","microbial-ecology","microbiome","regional-scale","subsurface"],"latest_commit_sha":null,"homepage":"","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/LLNL.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":null,"code_of_conduct":"CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2021-07-18T15:03:08.000Z","updated_at":"2022-04-06T02:36:35.000Z","dependencies_parsed_at":"2023-09-30T00:17:39.003Z","dependency_job_id":null,"html_url":"https://github.com/LLNL/2022_DVRFS_microbiome","commit_stats":{"total_commits":19,"total_committers":1,"mean_commits":19.0,"dds":0.0,"last_synced_commit":"fe2f4056125feabdeaea1615332693dd0e9f8c86"},"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LLNL%2F2022_DVRFS_microbiome","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LLNL%2F2022_DVRFS_microbiome/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LLNL%2F2022_DVRFS_microbiome/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LLNL%2F2022_DVRFS_microbiome/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/LLNL","download_url":"https://codeload.github.com/LLNL/2022_DVRFS_microbiome/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":241020654,"owners_count":19895474,"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":["groundwater","groundwater-flow","hydraulic-connectivity","microbial-communities","microbial-community-assembly","microbial-ecology","microbiome","regional-scale","subsurface"],"created_at":"2024-11-11T21:31:57.733Z","updated_at":"2026-06-12T11:31:31.775Z","avatar_url":"https://github.com/LLNL.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"These scripts (IM#: LLNL-CODE-823962) document the code used to analyze the Death Valley Regional Flow System (DVRFS) microbial community for a \u003ca href=\"https://www.sciencedirect.com/science/article/pii/S0048969722038657\"\u003emanuscript\u003c/a\u003e titled \"Subsurface microbial communities as a tool for characterizing regional-scale groundwater flow\". The R packages used for this manuscript can be found in the file \"Packages_and_Paths_microbe.r\". The associated scripts for figures/tables in the manuscript are:\n\n- 01.Dada2.r : Table S4\u003cbr\u003e\n- 02.FilteringOTUs.r : Table S11; Figure S1\u003cbr\u003e\n- 03.PhylogeneticTree.sh : None\u003cbr\u003e\n- 04.Barplots.r : Figure S5\u003cbr\u003e\n- 05.AlphaDiversity.r : Figure 3, Figure S6\u003cbr\u003e\n- 06.BetaDiversity.r : Figure 4, Figure S7, Table 1\u003cbr\u003e\n- 07.NetworkAnalysis.r : Figure 5, Figure S3, Figure S8, Table S6, Table S7 \u003cbr\u003e\n- 08.EcologicalProcess.r : Figure 6, Figure S2, Table S8 \u003cbr\u003e\n- Geochem.r : Figure 2, Table S2, Table S3, Table S9, Table S10\u003cbr\u003e\n\nMerino, N., Jackson, T.R., Campbell, J.H., Kersting, A.B., Sackett, J., Fisher, J.C., et al. (2022) Subsurface microbial communities as a tool for characterizing regional-scale groundwater flow. Science of The Total Environment 842: 156768. 10.1016/j.scitotenv.2022.156768\n\nOpen Source Distribution, under the terms of the LGPL, v3.0 license.\u003cbr\u003e\nThese code will not be updated once the manuscript has been accepted. \n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fllnl%2F2022_dvrfs_microbiome","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fllnl%2F2022_dvrfs_microbiome","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fllnl%2F2022_dvrfs_microbiome/lists"}