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adding comments about the data download and notebooks execution #29

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adding comments about the data download and notebooks execution #29

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18 changes: 6 additions & 12 deletions notebooks/10x_snRNASeq_tutorial_part_1.ipynb
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Expand Up @@ -10,7 +10,7 @@
"\n",
"The purpose of this set of notebooks is to provide an overview of the data, the file organization and how to combine data and metadata through example use cases.\n",
"\n",
"You need to be connected to the internet to run this notebook and that you have downloaded the example data via the getting started notebook."
"**You need to be connected to the internet to run this notebook and that you have downloaded the example data via the getting started notebook.**"
]
},
{
Expand Down Expand Up @@ -1283,9 +1283,7 @@
{
"cell_type": "code",
"execution_count": 20,
"metadata": {
"scrolled": false
},
"metadata": {},
"outputs": [
{
"data": {
Expand Down Expand Up @@ -2013,9 +2011,7 @@
{
"cell_type": "code",
"execution_count": 34,
"metadata": {
"scrolled": false
},
"metadata": {},
"outputs": [],
"source": [
"def plot_heatmap( df, fig_width = 8, fig_height = 4, cmap=plt.cm.magma_r, vmax=None) :\n",
Expand Down Expand Up @@ -2047,9 +2043,7 @@
{
"cell_type": "code",
"execution_count": 35,
"metadata": {
"scrolled": false
},
"metadata": {},
"outputs": [
{
"data": {
Expand Down Expand Up @@ -2243,7 +2237,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
Expand All @@ -2257,7 +2251,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.5"
"version": "3.10.9"
}
},
"nbformat": 4,
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12 changes: 5 additions & 7 deletions notebooks/10x_snRNASeq_tutorial_part_2a.ipynb
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Expand Up @@ -8,7 +8,7 @@
"\n",
"In part 1, we explore two examples looking at the expression of canonical neurotransmitter transporter genes and gene Tac2 in the thalamus. In this notebook, we will prepare data so that we can repeat the examples for all cells spanning the whole brain. This notebook takes ~ 5 minutes to run.\n",
"\n",
"The results from this notebook has already been cached and saved. As such, you can skip this notebook and continue with part 2b.\n",
"**The results from this notebook has already been cached and saved. Some of the cells might raise an error if you have not downloaded all of the data. As such, you can skip this notebook and continue with part 2b.**\n",
"\n",
"You need to be connected to the internet to run this notebook and that you have downloaded the all the log2 expression matrices associated with both the WMB-10Xv2, WMB-10Xv3 and WMB-10XMulti datasets."
]
Expand Down Expand Up @@ -75,9 +75,7 @@
{
"cell_type": "code",
"execution_count": 4,
"metadata": {
"scrolled": false
},
"metadata": {},
"outputs": [],
"source": [
"rpath = metadata['cell_metadata']['files']['csv']['relative_path']\n",
Expand Down Expand Up @@ -284,7 +282,7 @@
"\n",
"In this section, we explore two use cases. The first example looks at the expression of nine canonical neurotransmitter transporter genes and the second the expression of gene Tac2.\n",
"\n",
"To support these use cases, we will create a smaller submatrix (all cells and 10 genes) and write to file for resue in part 2b. *Note this operation takes around 5 minutes*."
"To support these use cases, we will create a smaller submatrix (all cells and 10 genes) and write to file for resue in part 2b. **Note this operation takes around 5 minutes and you might need to download more data. You can always skip this part and continue with part 2b.**"
]
},
{
Expand Down Expand Up @@ -585,7 +583,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
Expand All @@ -599,7 +597,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.5"
"version": "3.10.9"
}
},
"nbformat": 4,
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10 changes: 4 additions & 6 deletions notebooks/10x_snRNASeq_tutorial_part_2b.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@
"\n",
"We can continue to explore our examples looking at the expression of canonical neurotransmitter transporter genes and gene Tac2 over the whole brain. \n",
"\n",
"You need to be connected to the internet to run this notebook and that you have downloaded the example data via the getting started notebook."
"**You need to be connected to the internet to run this notebook and that you have downloaded the example data via the getting started notebook.**"
]
},
{
Expand Down Expand Up @@ -523,9 +523,7 @@
{
"cell_type": "code",
"execution_count": 22,
"metadata": {
"scrolled": false
},
"metadata": {},
"outputs": [
{
"data": {
Expand Down Expand Up @@ -625,7 +623,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
Expand All @@ -639,7 +637,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.5"
"version": "3.10.9"
}
},
"nbformat": 4,
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8 changes: 5 additions & 3 deletions notebooks/getting_started.ipynb
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Expand Up @@ -226,7 +226,9 @@
"source": [
"### Downloading all metadata directories\n",
"\n",
"Since the metadata directories are relatively small we will download all the metadata directories. We loop through the manifest and download each metadata directory using **[AWS CLI](https://aws.amazon.com/cli/)** sync command. This should take < 5 minutes."
"Since the metadata directories are relatively small we will download all the metadata directories. We loop through the manifest and download each metadata directory using **[AWS CLI](https://aws.amazon.com/cli/)** sync command. This should take < 5 minutes.\n",
"\n",
"**Please note that there are lines that you should uncomment to run the command to download the data.**"
]
},
{
Expand Down Expand Up @@ -468,7 +470,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
Expand All @@ -482,7 +484,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.5"
"version": "3.10.9"
}
},
"nbformat": 4,
Expand Down