{
  "id": 344816,
  "title": "Single-cell analysis workflow",
  "url": "/competitions/open-problems-multimodal/discussion/344816",
  "author_name": "Mikhael Manurung",
  "post_date": "2022-08-16T17:41:54.213000",
  "votes": 11,
  "comment_count": 0,
  "views": 0,
  "content": "<p>So far, most notebooks are using <code>pandas</code> to load and analyse the single-cell data. Here I introduced several python packages that are widely used for single-cell data analysis:</p>\n<ul>\n<li><a href=\"https://scanpy.readthedocs.io/en/stable/\" target=\"_blank\">scanpy</a></li>\n<li><a href=\"https://docs.scvi-tools.org/en/latest/index.html\" target=\"_blank\">scvi-tools</a></li>\n<li><a href=\"https://scprep.readthedocs.io/en/stable/reference.html\" target=\"_blank\">scprep</a></li>\n<li><a href=\"https://muon.readthedocs.io/en/latest/index.html\" target=\"_blank\">muon</a></li>\n</ul>\n<p>Muon, in particular, was made for multi-modal data analysis. You can also find several example workflows in the documentations of the respective packages.</p>\n<p>If you want to read a bit more on the overview of single-cell analysis best practices, you can find it<a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6582955/\" target=\"_blank\">here</a>, albeit it's quite outdated already and IIRC did not touch on multi-modal data analysis.</p>\n<p>This topic will be updated throughout the competition :)</p>",
  "messages": [
    {
      "id": 1901515,
      "postDate": "2022-08-16T17:41:54.213Z",
      "content": "<p>So far, most notebooks are using <code>pandas</code> to load and analyse the single-cell data. Here I introduced several python packages that are widely used for single-cell data analysis:</p>\n<ul>\n<li><a href=\"https://scanpy.readthedocs.io/en/stable/\" target=\"_blank\">scanpy</a></li>\n<li><a href=\"https://docs.scvi-tools.org/en/latest/index.html\" target=\"_blank\">scvi-tools</a></li>\n<li><a href=\"https://scprep.readthedocs.io/en/stable/reference.html\" target=\"_blank\">scprep</a></li>\n<li><a href=\"https://muon.readthedocs.io/en/latest/index.html\" target=\"_blank\">muon</a></li>\n</ul>\n<p>Muon, in particular, was made for multi-modal data analysis. You can also find several example workflows in the documentations of the respective packages.</p>\n<p>If you want to read a bit more on the overview of single-cell analysis best practices, you can find it<a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6582955/\" target=\"_blank\">here</a>, albeit it's quite outdated already and IIRC did not touch on multi-modal data analysis.</p>\n<p>This topic will be updated throughout the competition :)</p>",
      "rawMarkdown": "So far, most notebooks are using `pandas` to load and analyse the single-cell data. Here I introduced several python packages that are widely used for single-cell data analysis:\n- [scanpy](https://scanpy.readthedocs.io/en/stable/)\n- [scvi-tools](https://docs.scvi-tools.org/en/latest/index.html)\n- [scprep](https://scprep.readthedocs.io/en/stable/reference.html)\n- [muon](https://muon.readthedocs.io/en/latest/index.html)\n\nMuon, in particular, was made for multi-modal data analysis. You can also find several example workflows in the documentations of the respective packages.\n\nIf you want to read a bit more on the overview of single-cell analysis best practices, you can find it[here](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6582955/), albeit it's quite outdated already and IIRC did not touch on multi-modal data analysis.\n\nThis topic will be updated throughout the competition :)",
      "votes": 11
    }
  ],
  "comments": [],
  "raw_markdown_by_id": {
    "1901515": "So far, most notebooks are using `pandas` to load and analyse the single-cell data. Here I introduced several python packages that are widely used for single-cell data analysis:\n- [scanpy](https://scanpy.readthedocs.io/en/stable/)\n- [scvi-tools](https://docs.scvi-tools.org/en/latest/index.html)\n- [scprep](https://scprep.readthedocs.io/en/stable/reference.html)\n- [muon](https://muon.readthedocs.io/en/latest/index.html)\n\nMuon, in particular, was made for multi-modal data analysis. You can also find several example workflows in the documentations of the respective packages.\n\nIf you want to read a bit more on the overview of single-cell analysis best practices, you can find it[here](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6582955/), albeit it's quite outdated already and IIRC did not touch on multi-modal data analysis.\n\nThis topic will be updated throughout the competition :)"
  }
}