{
"cells": [
{
"cell_type": "markdown",
"metadata": {
"id": "view-in-github",
"colab_type": "text"
},
"source": [
""
]
},
{
"cell_type": "markdown",
"metadata": {
"id": "ziNMon68otdy"
},
"source": [
"# Symphonypy usage with your own reference"
]
},
{
"cell_type": "code",
"source": [
"!pip install scanpy[leiden] openTSNE symphonypy\n",
"!gdown \"1jW548g6ERFS0t7NywgyjRs6VaE5QwXbg&confirm=t\""
],
"metadata": {
"id": "yGeGn41HBUbf"
},
"execution_count": null,
"outputs": []
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/",
"height": 221
},
"id": "bsGMbgYeozIm",
"outputId": "99eeba99-f169-463b-f0bf-019004eedcf0"
},
"outputs": [
{
"output_type": "execute_result",
"data": {
"text/plain": [
" orig.ident lane donor time celltype.l1 celltype.l2 \\\n",
"L1_AAACCCACATCAGTCA P3_3 L1 P3 3 CD8 T CD8 TEM \n",
"L1_AAACCCATCCACACCT P3_3 L1 P3 3 CD8 T CD8 Naive \n",
"L1_AAACCCATCTGCGGAC P1_0 L1 P1 0 CD4 T CD4 TCM \n",
"L1_AAACCCATCTTAAGGC P2_3 L1 P2 3 CD4 T CD4 CTL \n",
"L1_AAACGAAAGATAACAC P2_3 L1 P2 3 B B naive \n",
"\n",
" celltype.l3 Phase \n",
"L1_AAACCCACATCAGTCA CD8 TEM_1 G1 \n",
"L1_AAACCCATCCACACCT CD8 Naive S \n",
"L1_AAACCCATCTGCGGAC CD4 TCM_1 S \n",
"L1_AAACCCATCTTAAGGC CD4 CTL S \n",
"L1_AAACGAAAGATAACAC B naive kappa S "
],
"text/html": [
"\n",
"
| \n", " | orig.ident | \n", "lane | \n", "donor | \n", "time | \n", "celltype.l1 | \n", "celltype.l2 | \n", "celltype.l3 | \n", "Phase | \n", "
|---|---|---|---|---|---|---|---|---|
| L1_AAACCCACATCAGTCA | \n", "P3_3 | \n", "L1 | \n", "P3 | \n", "3 | \n", "CD8 T | \n", "CD8 TEM | \n", "CD8 TEM_1 | \n", "G1 | \n", "
| L1_AAACCCATCCACACCT | \n", "P3_3 | \n", "L1 | \n", "P3 | \n", "3 | \n", "CD8 T | \n", "CD8 Naive | \n", "CD8 Naive | \n", "S | \n", "
| L1_AAACCCATCTGCGGAC | \n", "P1_0 | \n", "L1 | \n", "P1 | \n", "0 | \n", "CD4 T | \n", "CD4 TCM | \n", "CD4 TCM_1 | \n", "S | \n", "
| L1_AAACCCATCTTAAGGC | \n", "P2_3 | \n", "L1 | \n", "P2 | \n", "3 | \n", "CD4 T | \n", "CD4 CTL | \n", "CD4 CTL | \n", "S | \n", "
| L1_AAACGAAAGATAACAC | \n", "P2_3 | \n", "L1 | \n", "P2 | \n", "3 | \n", "B | \n", "B naive | \n", "B naive kappa | \n", "S | \n", "