{"action":"created","issue":{"url":"https://api.github.com/repos/Bioconductor/Contributions/issues/943","repository_url":"https://api.github.com/repos/Bioconductor/Contributions","labels_url":"https://api.github.com/repos/Bioconductor/Contributions/issues/943/labels{/name}","comments_url":"https://api.github.com/repos/Bioconductor/Contributions/issues/943/comments","events_url":"https://api.github.com/repos/Bioconductor/Contributions/issues/943/events","html_url":"https://github.com/Bioconductor/Contributions/issues/943","id":385310272,"node_id":"MDU6SXNzdWUzODUzMTAyNzI=","number":943,"title":"NPA","user":{"login":"sgubianpm","id":17434537,"node_id":"MDQ6VXNlcjE3NDM0NTM3","avatar_url":"https://avatars0.githubusercontent.com/u/17434537?v=4","gravatar_id":"","url":"https://api.github.com/users/sgubianpm","html_url":"https://github.com/sgubianpm","followers_url":"https://api.github.com/users/sgubianpm/followers","following_url":"https://api.github.com/users/sgubianpm/following{/other_user}","gists_url":"https://api.github.com/users/sgubianpm/gists{/gist_id}","starred_url":"https://api.github.com/users/sgubianpm/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sgubianpm/subscriptions","organizations_url":"https://api.github.com/users/sgubianpm/orgs","repos_url":"https://api.github.com/users/sgubianpm/repos","events_url":"https://api.github.com/users/sgubianpm/events{/privacy}","received_events_url":"https://api.github.com/users/sgubianpm/received_events","type":"User","site_admin":false},"labels":[{"id":335833554,"node_id":"MDU6TGFiZWwzMzU4MzM1NTQ=","url":"https://api.github.com/repos/Bioconductor/Contributions/labels/2.%20review%20in%20progress","name":"2. review in progress","color":"1881c2","default":false},{"id":335833865,"node_id":"MDU6TGFiZWwzMzU4MzM4NjU=","url":"https://api.github.com/repos/Bioconductor/Contributions/labels/WARNINGS","name":"WARNINGS","color":"dd8822","default":false}],"state":"open","locked":false,"assignee":{"login":"lshep","id":18724380,"node_id":"MDQ6VXNlcjE4NzI0Mzgw","avatar_url":"https://avatars3.githubusercontent.com/u/18724380?v=4","gravatar_id":"","url":"https://api.github.com/users/lshep","html_url":"https://github.com/lshep","followers_url":"https://api.github.com/users/lshep/followers","following_url":"https://api.github.com/users/lshep/following{/other_user}","gists_url":"https://api.github.com/users/lshep/gists{/gist_id}","starred_url":"https://api.github.com/users/lshep/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lshep/subscriptions","organizations_url":"https://api.github.com/users/lshep/orgs","repos_url":"https://api.github.com/users/lshep/repos","events_url":"https://api.github.com/users/lshep/events{/privacy}","received_events_url":"https://api.github.com/users/lshep/received_events","type":"User","site_admin":false},"assignees":[{"login":"lshep","id":18724380,"node_id":"MDQ6VXNlcjE4NzI0Mzgw","avatar_url":"https://avatars3.githubusercontent.com/u/18724380?v=4","gravatar_id":"","url":"https://api.github.com/users/lshep","html_url":"https://github.com/lshep","followers_url":"https://api.github.com/users/lshep/followers","following_url":"https://api.github.com/users/lshep/following{/other_user}","gists_url":"https://api.github.com/users/lshep/gists{/gist_id}","starred_url":"https://api.github.com/users/lshep/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lshep/subscriptions","organizations_url":"https://api.github.com/users/lshep/orgs","repos_url":"https://api.github.com/users/lshep/repos","events_url":"https://api.github.com/users/lshep/events{/privacy}","received_events_url":"https://api.github.com/users/lshep/received_events","type":"User","site_admin":false}],"milestone":null,"comments":11,"created_at":"2018-11-28T15:04:43Z","updated_at":"2018-12-10T17:31:26Z","closed_at":null,"author_association":"NONE","body":"Update the following URL to point to the GitHub repository of\r\nthe package you wish to submit to _Bioconductor_\r\n\r\n- Repository: https://github.com/pmpsa-hpc/NPAModels\r\n\r\nConfirm the following by editing each check box to '[x]'\r\n\r\n- [X] I understand that by submitting my package to _Bioconductor_,\r\n  the package source and all review commentary are visible to the\r\n  general public.\r\n\r\n- [X] I have read the _Bioconductor_ [Package Submission][2]\r\n  instructions. My package is consistent with the _Bioconductor_\r\n  [Package Guidelines][1].\r\n\r\n- [X] I understand that a minimum requirement for package acceptance \r\n  is to pass R CMD check and R CMD BiocCheck with no ERROR or WARNINGS. \r\n  Passing these checks does not result in automatic acceptance. The \r\n  package will then undergo a formal review and recommendations for \r\n  acceptance regarding other Bioconductor standards will be addressed.\r\n\r\n- [X] My package addresses statistical or bioinformatic issues related\r\n  to the analysis and comprehension of high throughput genomic data.\r\n\r\n- [X] I am committed to the long-term maintenance of my package. This\r\n  includes monitoring the [support site][3] for issues that users may\r\n  have, subscribing to the [bioc-devel][4] mailing list to stay aware\r\n  of developments in the _Bioconductor_ community, responding promptly\r\n  to requests for updates from the Core team in response to changes in\r\n  _R_ or underlying software.\r\n\r\nI am familiar with the essential aspects of _Bioconductor_ software\r\nmanagement, including:\r\n\r\n- [X] The 'devel' branch for new packages and features.\r\n- [X] The stable 'release' branch, made available every six\r\n      months, for bug fixes.\r\n- [X] _Bioconductor_ version control using [Git][5]\r\n  (optionally [via GitHub][6]).\r\n\r\nFor help with submitting your package, please subscribe and post questions\r\nto the [bioc-devel][4] mailing list.\r\n\r\n[1]: https://bioconductor.org/developers/package-guidelines/\r\n[2]: https://bioconductor.org/developers/package-submission/\r\n[3]: https://support.bioconductor.org\r\n[4]: https://stat.ethz.ch/mailman/listinfo/bioc-devel\r\n[5]: http://bioconductor.org/developers/how-to/git/\r\n[6]: http://bioconductor.org/developers/how-to/git/sync-existing-repositories/\r\n"},"comment":{"url":"https://api.github.com/repos/Bioconductor/Contributions/issues/comments/445901444","html_url":"https://github.com/Bioconductor/Contributions/issues/943#issuecomment-445901444","issue_url":"https://api.github.com/repos/Bioconductor/Contributions/issues/943","id":445901444,"node_id":"MDEyOklzc3VlQ29tbWVudDQ0NTkwMTQ0NA==","user":{"login":"bioc-issue-bot","id":17282096,"node_id":"MDQ6VXNlcjE3MjgyMDk2","avatar_url":"https://avatars0.githubusercontent.com/u/17282096?v=4","gravatar_id":"","url":"https://api.github.com/users/bioc-issue-bot","html_url":"https://github.com/bioc-issue-bot","followers_url":"https://api.github.com/users/bioc-issue-bot/followers","following_url":"https://api.github.com/users/bioc-issue-bot/following{/other_user}","gists_url":"https://api.github.com/users/bioc-issue-bot/gists{/gist_id}","starred_url":"https://api.github.com/users/bioc-issue-bot/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bioc-issue-bot/subscriptions","organizations_url":"https://api.github.com/users/bioc-issue-bot/orgs","repos_url":"https://api.github.com/users/bioc-issue-bot/repos","events_url":"https://api.github.com/users/bioc-issue-bot/events{/privacy}","received_events_url":"https://api.github.com/users/bioc-issue-bot/received_events","type":"User","site_admin":false},"created_at":"2018-12-10T17:31:26Z","updated_at":"2018-12-10T17:31:26Z","author_association":"COLLABORATOR","body":"Hi @sgubianpm,\n\nStarting build on additional package https://github.com/pmpsa-hpc/NPA.\n\n**IMPORTANT**: Please read [the instructions][1] for setting up a\npush hook on your repository, or further changes to your\nadditional package repository will NOT trigger a new build.\n\nThe DESCRIPTION file of this additional package is:\n\n```\nPackage: NPA\nType: Package\nTitle: Network Perturbation Amplitude\nVersion: 0.99.0\nDate: 2018-01-29\nAuthor: Florian Martin <Florian.Martin@pmi.com>, Sylvain Gubian\n<Sylvain.Gubian@pmi.com>\nMaintainer: Sylvain Gubian <DL.RSupport@pmi.com>\nDepends:\nR (>= 3.5),\nR6\nImports:\ngrid,\ngrDevices,\ngraphics,\nstats,\nutils,\nggplot2,\nplotrix,\ngplots,\nRColorBrewer,\nRGraph2js,\nreshape2,\nstringr,\nmethods,\nscales,\ngraph,\nRgraphviz,\ndnet,\nigraph,\nNPAModels\nDescription: Scoring method of Biological Networks based on NPA (Network\nPerturbation Amplitude) algorithm. The methodology implemented enables\nto translate the gene expression fold-changes into differential values\nfor each network node, and to summarize this at the network level to\nprovide a quantitative assessment of the degree of perturbation of the\nnetwork model, the Network Perturbation Amplitude (NPA).\nCombining multiple relevant network models, the overall biological impact\n(BIF) of a perturbing agent, the Biological Impact Factor, can be\ncalculated by aggregating individual NPA scores.\nLicense: file LICENSE\nLazyLoad: yes\nRoxygenNote: 6.1.1\nCollate:\n'BIF-class.R'\n'COPD1.R'\n'utils.R'\n'colorscale.R'\n'getNPALE.R'\n'getNPAmodulesGlobal.R'\n'NPA-class.R'\n'NPA.R'\n'imageplot_gg.R'\n'extract_npas.R'\n'getBIF.R'\n'NPAList-class.R'\n'NPAallrename.R'\n'NPAheatmap.R'\n'NPAsubset.R'\n'getNPALEtable2.R'\n'as.matrix.R'\n'starplot.R'\n'barplotBIF.R'\n'barplotNPAGG.R'\n'barplotNPA.R'\n'barplotNPA3.R'\n'barplot.R'\n'computeNPA.R'\n'drawNPAjs.R'\n'visNet2.R'\n'drawNPAmodule.R'\n'getBIF0weighted.R'\n'getBIFdist.R'\n'getC.R'\n'getLE.R'\n'getsplit.R'\n'getNPAmodules.R'\n'getNPAnames.R'\n'getNets.R'\n'getNets1.R'\n'getNets2.R'\n'getWeightedBIF.R'\n'npa_example.R'\n'onLoad.R'\n'plotNPAmodulesGlobal.R'\n'starplotBIFnetworks.R'\n'starplotBIFcontrasts.R'\n'plot.R'\n'subset.R'\nbiocViews: DifferentialExpression, Visualization, Network, GraphAndNetwork, MathematicalBiology, SystemsBiology, Transcriptomics, GeneExpression\nSuggests:\nknitr,\nrmarkdown,\ntestthat\nVignetteBuilder: knitr\n\n```\n[1]: https://github.com/Bioconductor/Contributions/blob/master/CONTRIBUTING.md\n"}}
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