{"id":23046176,"url":"https://github.com/cpanse/nestlink","last_synced_at":"2026-03-07T06:31:21.562Z","repository":{"id":88060313,"uuid":"45106873","full_name":"cpanse/NestLink","owner":"cpanse","description":"Engineered Peptide Barcodes for In-Depth Analyses of Binding Protein Ensembles  - replication code","archived":false,"fork":false,"pushed_at":"2022-05-10T08:12:46.000Z","size":40438,"stargazers_count":5,"open_issues_count":0,"forks_count":1,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-04-03T03:32:47.483Z","etag":null,"topics":["bioconductor","mass-spectrometry","prediction","retention-time","rpackage","sequencing","simulation"],"latest_commit_sha":null,"homepage":"https://bioconductor.org/packages/NestLink","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/cpanse.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":"2015-10-28T11:06:52.000Z","updated_at":"2023-06-22T20:17:11.000Z","dependencies_parsed_at":"2023-03-02T01:00:11.306Z","dependency_job_id":null,"html_url":"https://github.com/cpanse/NestLink","commit_stats":{"total_commits":525,"total_committers":4,"mean_commits":131.25,"dds":"0.25142857142857145","last_synced_commit":"d69a07433a45702f0d30896d8cab38d027210f1e"},"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"purl":"pkg:github/cpanse/NestLink","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cpanse%2FNestLink","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cpanse%2FNestLink/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cpanse%2FNestLink/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cpanse%2FNestLink/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/cpanse","download_url":"https://codeload.github.com/cpanse/NestLink/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cpanse%2FNestLink/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":270505601,"owners_count":24596501,"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":"2025-08-14T02:00:10.309Z","response_time":75,"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":["bioconductor","mass-spectrometry","prediction","retention-time","rpackage","sequencing","simulation"],"created_at":"2024-12-15T21:30:18.650Z","updated_at":"2026-03-07T06:31:21.513Z","avatar_url":"https://github.com/cpanse.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# NestLink \n\nEngineered Peptide Barcodes for In-Depth Analyses of Binding Protein Ensembles\n\n\u003chr\u003e\n\navailable for download in the 'Devel' version of Bioconductor using `BiocManager::install(\"NestLink\")`.\nThe package 'landing page' is available at https://bioconductor.org/packages/NestLink\n(since 2019-01-14)\n\n\u003chr\u003e\n\n## 1. System requirements\n\n### Software dependencies\n\n- install R (\u003e= 3.6)\n\n- install Bioconductor (\u003e=3.9)\n\n## 2. Installation guide\n\nrun an R session and execute the following R code snippet\n\n```{r}\nif (!requireNamespace(\"BiocManager\", quietly = TRUE))\n    install.packages(\"BiocManager\")\n    \nBiocManager::install(\"cpanse/NestLink\", version = \"3.9\")  \n```\n\nor using [docker](https://cloud.docker.com/u/cpanse/repository/docker/cpanse/nestlink)\n\n```\ndocker pull cpanse/nestlink \\\n  \u0026\u0026 docker run -a stdin -a stdout -i -t cpanse/nestlink /scratch/R-devel/bin/R\n```\n\n\n**Typical install time** - \nbased on the [Dockerfile](inst/scripts/Dockerfile) the install snippet above \ntook 19m46.464s on a linux server (RAID6, Intel(R) Xeon(R) CPU E5-2698 v3 @ 2.30GHz) and one hour on dockerhub.\n\nAs an alternative you can also consider the latest [release](https://github.com/cpanse/NestLink/releases).\n\n### Versions the software has been tested on\n\n|platform|NestLink version|platform version|R version|note|\n| :------- |:---------------|:---------------| :-------|:------- |\n|Linux     | 0.99.51 | Debian 10 ([buster](https://www.debian.org/releases/testing/releasenotes)) | R 3.5.1, Bioconductor version 3.8| CP |\n|Microsoft | 0.99.51 | Server 2012 R2 x64| R 3.5.0, Bioconductor version 3.7||\n| macOS High| 0.99.51 | Sierra 10.13.4| R 3.4.2||\n\n## 3. Demonstration / Documentation\n\nInstructions to run on data and expected output is described in the package's \nvignettes.\n\n```{r}\nbrowseVignettes('NestLink')\n```\n\nplease study the vignettes in the following order:\n\n0. Derive Peptide FlyCodes by Conducting Random Experiment  \n1. NGS filtering workflow to get high quality FlyCode and Nanobody sequences  \n2. FASTA p1875 db10 - ESP / SSRC prediction - Summary \n3. Compare Predicted and Measured FlyCodes (F255744).  \n4. Control experiment to assess robustness of protein detection via flycodes \n\n\nExpected run time for the vignette build is less than 5 minutes on a today's desktop computer.\n\n## 4. Instructions for use\n\nread the vignettes.\n\n```{r}\nbrowseVignettes('NestLink')\n```\n\n## References \n\n- [project p1875 at the Functional Genomics Center Zurich](https://fgcz-bfabric.uzh.ch/bfabric/userlab/show-project.html?id=1875)\n\n- [bioRxiv 2018/03/23/287813](https://www.biorxiv.org/content/early/2018/03/23/287813)\n\n- [DOI:10.1038/s41592-019-0389-8](https://www.nature.com/articles/s41592-019-0389-8)\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcpanse%2Fnestlink","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcpanse%2Fnestlink","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcpanse%2Fnestlink/lists"}