{
  "id": 443871,
  "title": "Single cell RNA seq part of data -- conversion to ->  sparse matrix and adata (standard bioinfo format)",
  "url": "/competitions/open-problems-single-cell-perturbations/discussion/443871",
  "author_name": "Alexander Chervov",
  "post_date": "2023-09-29T07:46:59.110000",
  "votes": 6,
  "comment_count": 0,
  "views": 0,
  "content": "<p>For those who like  standard bioinfo formats:<br>\nHere is  scanpy  pipeline (with adata) notebook: <a href=\"https://www.kaggle.com/alexandervc/op2-rna-seq-data-scanpy-adata-cell-cycle/\" target=\"_blank\">https://www.kaggle.com/alexandervc/op2-rna-seq-data-scanpy-adata-cell-cycle/</a></p>\n<p>And here is conversion from parquet to scipy sparse matrix:<br>\n<a href=\"https://www.kaggle.com/code/alexandervc/op2-rna-seq-data-to-sparse-matrix/\" target=\"_blank\">https://www.kaggle.com/code/alexandervc/op2-rna-seq-data-to-sparse-matrix/</a> <br>\n(Take data from \"output\" of that notebook - pay attention Kaggle allows to \"add data\" to your notebooks, not only from Kaggle datasets, but from the notebooks (i.e. from their output section). </p>",
  "messages": [
    {
      "id": 2460931,
      "postDate": "2023-09-29T07:46:59.110Z",
      "content": "<p>For those who like  standard bioinfo formats:<br>\nHere is  scanpy  pipeline (with adata) notebook: <a href=\"https://www.kaggle.com/alexandervc/op2-rna-seq-data-scanpy-adata-cell-cycle/\" target=\"_blank\">https://www.kaggle.com/alexandervc/op2-rna-seq-data-scanpy-adata-cell-cycle/</a></p>\n<p>And here is conversion from parquet to scipy sparse matrix:<br>\n<a href=\"https://www.kaggle.com/code/alexandervc/op2-rna-seq-data-to-sparse-matrix/\" target=\"_blank\">https://www.kaggle.com/code/alexandervc/op2-rna-seq-data-to-sparse-matrix/</a> <br>\n(Take data from \"output\" of that notebook - pay attention Kaggle allows to \"add data\" to your notebooks, not only from Kaggle datasets, but from the notebooks (i.e. from their output section). </p>",
      "rawMarkdown": "For those who like  standard bioinfo formats:\nHere is  scanpy  pipeline (with adata) notebook: https://www.kaggle.com/alexandervc/op2-rna-seq-data-scanpy-adata-cell-cycle/\n\nAnd here is conversion from parquet to scipy sparse matrix:\nhttps://www.kaggle.com/code/alexandervc/op2-rna-seq-data-to-sparse-matrix/ \n(Take data from \"output\" of that notebook - pay attention Kaggle allows to \"add data\" to your notebooks, not only from Kaggle datasets, but from the notebooks (i.e. from their output section). \n",
      "votes": 6
    }
  ],
  "comments": [],
  "raw_markdown_by_id": {
    "2460931": "For those who like  standard bioinfo formats:\nHere is  scanpy  pipeline (with adata) notebook: https://www.kaggle.com/alexandervc/op2-rna-seq-data-scanpy-adata-cell-cycle/\n\nAnd here is conversion from parquet to scipy sparse matrix:\nhttps://www.kaggle.com/code/alexandervc/op2-rna-seq-data-to-sparse-matrix/ \n(Take data from \"output\" of that notebook - pay attention Kaggle allows to \"add data\" to your notebooks, not only from Kaggle datasets, but from the notebooks (i.e. from their output section). \n"
  }
}