{"action":"created","issue":{"url":"https://api.github.com/repos/mikelove/tximport/issues/25","repository_url":"https://api.github.com/repos/mikelove/tximport","labels_url":"https://api.github.com/repos/mikelove/tximport/issues/25/labels{/name}","comments_url":"https://api.github.com/repos/mikelove/tximport/issues/25/comments","events_url":"https://api.github.com/repos/mikelove/tximport/issues/25/events","html_url":"https://github.com/mikelove/tximport/issues/25","id":376872024,"node_id":"MDU6SXNzdWUzNzY4NzIwMjQ=","number":25,"title":"sparse matrix support?","user":{"login":"koenvandenberge","id":10134844,"node_id":"MDQ6VXNlcjEwMTM0ODQ0","avatar_url":"https://avatars3.githubusercontent.com/u/10134844?v=4","gravatar_id":"","url":"https://api.github.com/users/koenvandenberge","html_url":"https://github.com/koenvandenberge","followers_url":"https://api.github.com/users/koenvandenberge/followers","following_url":"https://api.github.com/users/koenvandenberge/following{/other_user}","gists_url":"https://api.github.com/users/koenvandenberge/gists{/gist_id}","starred_url":"https://api.github.com/users/koenvandenberge/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/koenvandenberge/subscriptions","organizations_url":"https://api.github.com/users/koenvandenberge/orgs","repos_url":"https://api.github.com/users/koenvandenberge/repos","events_url":"https://api.github.com/users/koenvandenberge/events{/privacy}","received_events_url":"https://api.github.com/users/koenvandenberge/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2018-11-02T16:04:23Z","updated_at":"2018-11-02T20:14:39Z","closed_at":null,"author_association":"NONE","body":"I was wondering whether it would possible to support sparse matrices as output of tximport.\r\nThis might make tximport more attractive for people working with scRNA-seq data.\r\n\r\nI'm currently running into problems when importing >400 single cells because of memory limits.\r\nSince the memory issues occur while importing the cells, converting the data to sparse format based on the `SummarizedExperiment` would not help because I can't get up to that point yet.\r\n\r\nA current solution is to import the data in parts, and convert those to sparse matrices.\r\n"},"comment":{"url":"https://api.github.com/repos/mikelove/tximport/issues/comments/435495866","html_url":"https://github.com/mikelove/tximport/issues/25#issuecomment-435495866","issue_url":"https://api.github.com/repos/mikelove/tximport/issues/25","id":435495866,"node_id":"MDEyOklzc3VlQ29tbWVudDQzNTQ5NTg2Ng==","user":{"login":"mikelove","id":69203,"node_id":"MDQ6VXNlcjY5MjAz","avatar_url":"https://avatars2.githubusercontent.com/u/69203?v=4","gravatar_id":"","url":"https://api.github.com/users/mikelove","html_url":"https://github.com/mikelove","followers_url":"https://api.github.com/users/mikelove/followers","following_url":"https://api.github.com/users/mikelove/following{/other_user}","gists_url":"https://api.github.com/users/mikelove/gists{/gist_id}","starred_url":"https://api.github.com/users/mikelove/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mikelove/subscriptions","organizations_url":"https://api.github.com/users/mikelove/orgs","repos_url":"https://api.github.com/users/mikelove/repos","events_url":"https://api.github.com/users/mikelove/events{/privacy}","received_events_url":"https://api.github.com/users/mikelove/received_events","type":"User","site_admin":false},"created_at":"2018-11-02T20:14:39Z","updated_at":"2018-11-02T20:14:39Z","author_association":"OWNER","body":"Setting aside the inference stuff (we're working on this, but side topic), we've tried to set it up so *tximport* has no dependencies to encourage broad adoption (developers don't want too many upstream dependencies) and *tximeta* builds the rich S4 objects. So I'm thinking *tximport* would give back a more basic object like a sparse matrix as implemented in *Matrix* package (and this would only be a Suggests). I think I can whip this up soon-ish. Meanwhile, we also are looking into *tximport* importing `alevin` output, which I should also find time to implement.\r\n\r\nIt seems simple enough for the point estimates, but would take some more time for the inferential replicates."}}
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