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"\n",
"# Summary\n",
"\n",
"The purpose of this JupyterHub is to let the community to retrieve public data at ease. For example, \n",
"1. you can retrieve the expression of a gene of >400,000 public sequencing profiles in < 1 second, or \n",
"2. extract the allelic read counts of a particular sequencing profile in < 1 second. \n",
"\n",
"In order to do so, we provide:\n",
"1. a single data matrix for each omic layer for each species that spans a total of >400k sequencing runs from all the public studies, which is done by reprocessing petabytes worth of sequencing data \n",
"2. a biological metadata file that describes the relationships between the sequencing runs and also the keywords extracted from over 3 million free text annotations using NLP.\n",
"3. a technical metadata file that describes the relationships between the sequencing runs.\n",
"\n",
"\n",
"\n",
"\n",
"\n",
"# Query and analyze the reprocessed data\n",
"* [RNA-seq](./RNAseqQuerying.ipynb)\n",
"* [Microbe](./MicrobeQuerying.ipynb)\n",
"* [Allelic read count](./plotAllelicReadCount.ipynb) \n",
"\n",
"### Example data loading\n",
"* [Loading variant data quantified in allelic read counts](./loadAllelicReadCountBySrrId.ipynb)\n",
"* [Loading RNA-seq data quantified in transcript counts](./loadingRNAseqByGene.ipynb)\n",
"* [Loading in all the technical and biological metadata](./loadMetaData_hub.ipynb)\n"
]
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"source": [
"# Auxilary\n",
"\n",
"### [Click here to switch the interface to Jupyter Lab](../../lab/)\n",
"It's quite a bit easier to use IMHO. "
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Feel free to email at skymap-info@googlegroups.com if you have any questions\n",
"\n",
"* Homepage: http://hannahcarterlab.org/jupyterhub"
]
}
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