{"action":"created","issue":{"url":"https://api.github.com/repos/cytomining/cytominergallery/issues/56","repository_url":"https://api.github.com/repos/cytomining/cytominergallery","labels_url":"https://api.github.com/repos/cytomining/cytominergallery/issues/56/labels{/name}","comments_url":"https://api.github.com/repos/cytomining/cytominergallery/issues/56/comments","events_url":"https://api.github.com/repos/cytomining/cytominergallery/issues/56/events","html_url":"https://github.com/cytomining/cytominergallery/issues/56","id":355564702,"node_id":"MDU6SXNzdWUzNTU1NjQ3MDI=","number":56,"title":"Dataset for Nat Methods paper + code","user":{"login":"eoziolor","id":29739817,"node_id":"MDQ6VXNlcjI5NzM5ODE3","avatar_url":"https://avatars3.githubusercontent.com/u/29739817?v=4","gravatar_id":"","url":"https://api.github.com/users/eoziolor","html_url":"https://github.com/eoziolor","followers_url":"https://api.github.com/users/eoziolor/followers","following_url":"https://api.github.com/users/eoziolor/following{/other_user}","gists_url":"https://api.github.com/users/eoziolor/gists{/gist_id}","starred_url":"https://api.github.com/users/eoziolor/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/eoziolor/subscriptions","organizations_url":"https://api.github.com/users/eoziolor/orgs","repos_url":"https://api.github.com/users/eoziolor/repos","events_url":"https://api.github.com/users/eoziolor/events{/privacy}","received_events_url":"https://api.github.com/users/eoziolor/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2018-08-30T12:33:52Z","updated_at":"2018-09-19T19:17:49Z","closed_at":null,"author_association":"NONE","body":"Hi!\r\n\r\nFirst of all than you for this wonderful set of tools. This absolutely moves the field miles ahead in ability of new people to get up and going on image analysis.\r\n\r\nOne things that I found myself needing is a way to replicate your work in the paper. The dataset you provide for training is comprised of 14K cells, rather than the one of 150K from the paper. As well there are many great visualizations you accomplish in the paper that are not shown in some of the vignettes (like heatmaps of pairwise comparisons or heatmaps of plate setup), which can be VERY useful to start with. If you could provide the workflow from the paper with the original dataset, that would be absolutely wonderful!\r\n\r\nThank you!\r\n\r\n-Elias"},"comment":{"url":"https://api.github.com/repos/cytomining/cytominergallery/issues/comments/422925995","html_url":"https://github.com/cytomining/cytominergallery/issues/56#issuecomment-422925995","issue_url":"https://api.github.com/repos/cytomining/cytominergallery/issues/56","id":422925995,"node_id":"MDEyOklzc3VlQ29tbWVudDQyMjkyNTk5NQ==","user":{"login":"shntnu","id":1210428,"node_id":"MDQ6VXNlcjEyMTA0Mjg=","avatar_url":"https://avatars0.githubusercontent.com/u/1210428?v=4","gravatar_id":"","url":"https://api.github.com/users/shntnu","html_url":"https://github.com/shntnu","followers_url":"https://api.github.com/users/shntnu/followers","following_url":"https://api.github.com/users/shntnu/following{/other_user}","gists_url":"https://api.github.com/users/shntnu/gists{/gist_id}","starred_url":"https://api.github.com/users/shntnu/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/shntnu/subscriptions","organizations_url":"https://api.github.com/users/shntnu/orgs","repos_url":"https://api.github.com/users/shntnu/repos","events_url":"https://api.github.com/users/shntnu/events{/privacy}","received_events_url":"https://api.github.com/users/shntnu/received_events","type":"User","site_admin":false},"created_at":"2018-09-19T19:17:49Z","updated_at":"2018-09-19T19:17:49Z","author_association":"COLLABORATOR","body":"Figure 5 was generated using a different dataset, not BBBC021. \r\n\r\nI propose you skip that and work on Fig 6 instead\r\n\r\nhere are the packages / functions you will need\r\n6a - `heatmap.2::heatmap.2` on the treatment profiles \r\n6b - `stats::prcomp` on single cell data, subsampled\r\n6c - `tsne::tsne` on single cell data, subsampled\r\n6d - `spade` package on single cell data, subsampled"}}
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