{"componentChunkName":"component---src-templates-blog-post-js","path":"/monocle3_on_colab/","result":{"data":{"site":{"siteMetadata":{"title":"tigue.com"}},"markdownRemark":{"id":"30d665c0-c1da-54e0-afd0-cac42a6d88df","excerpt":"Monocle 3 is “an analysis toolkit for single-cell RNA-seq.” It is MIT code out of Seattle’s Seattle Lake Union area. The source code is all R. I hacked on Colab…","html":"<p><span\n      class=\"gatsby-resp-image-wrapper\"\n      style=\"position: relative; display: block; margin-left: auto; margin-right: auto;  max-width: 1000px;\"\n    >\n      <a\n    class=\"gatsby-resp-image-link\"\n    href=\"/static/d6a84a5aeb8836fc30602127f3e10b52/f5429/monocle_cover_image.png\"\n    style=\"display: block\"\n    target=\"_blank\"\n    rel=\"noopener\"\n  >\n    <span\n    class=\"gatsby-resp-image-background-image\"\n    style=\"padding-bottom: 33.63197794624397%; position: relative; bottom: 0; left: 0; background-image: url('data:image/png;base64,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'); background-size: cover; display: block;\"\n  ></span>\n  <img\n        class=\"gatsby-resp-image-image\"\n        alt=\"monocle cover image\"\n        title=\"monocle cover image\"\n        src=\"/static/d6a84a5aeb8836fc30602127f3e10b52/5d675/monocle_cover_image.png\"\n        srcset=\"/static/d6a84a5aeb8836fc30602127f3e10b52/1abb1/monocle_cover_image.png 250w,\n/static/d6a84a5aeb8836fc30602127f3e10b52/7217d/monocle_cover_image.png 500w,\n/static/d6a84a5aeb8836fc30602127f3e10b52/5d675/monocle_cover_image.png 1000w,\n/static/d6a84a5aeb8836fc30602127f3e10b52/f5429/monocle_cover_image.png 1451w\"\n        sizes=\"(max-width: 1000px) 100vw, 1000px\"\n        loading=\"lazy\"\n      />\n  </a>\n    </span></p>\n<p><a href=\"https://cole-trapnell-lab.github.io/monocle3/\">Monocle 3</a> is “an analysis toolkit for single-cell RNA-seq.” It is <a href=\"https://github.com/cole-trapnell-lab/monocle3/blob/master/LICENSE.md\">MIT</a> code out of Seattle’s Seattle Lake Union area. The source code is all R.</p>\n<p>I hacked on Colab to see if I could get it to run Monocle3. The experiment went pretty well.</p>\n<p><a href=\"https://colab.research.google.com/drive/1Pj62n18qRb9DxPKM6L-PRdxV0-LYWk-P#scrollTo=DVxk3ON3J7Gy\" ><img alt=\"Open In Colab\" src=\"https://colab.research.google.com/assets/colab-badge.svg\" width=\"23%\"></p>\n<p>Migth as well use the above OpenInColab button to check it out but\nthe code can also be found on GitHub in the repo, [@reconstrue/single<em>cell</em>on<em>colab](https://github.com/reconstrue/single</em>cell<em>on</em>colab/tree/master/tools/monocle)</p>","frontmatter":{"title":"Monocle3 on Colab","date":"February 02, 2020","description":"TODO: a discription for cover card"}}},"pageContext":{"isCreatedByStatefulCreatePages":false,"slug":"/monocle3_on_colab/","previous":{"fields":{"slug":"/allensdk_for_training_skeletonizers/"},"frontmatter":{"title":"Traing Data for Neuron Reconstructors"}},"next":{"fields":{"slug":"/jupyter_book_notes/"},"frontmatter":{"title":"Jupyter Books' Many Manifestations of a Notebook"}}}}}