Update the template

.gitignore

@@ -132,15 +132,25 @@ dmypy.json
 *.csv
 *.pickle
 *.h5ad
+*.RData
 *.loom
 *.pdf
+*.eps
 *.png
 *.jpg
 *.jpeg
 *.svg
 *.mtx
 *.txt
 *.rds
+*.npz
+*.h5
+*.txt.gz
+*.gmt
+*.gmx
+
+data/
+figures/
 
 # OS specifics
 **.DS_Store

LICENSE

@@ -1,7 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2020, Theis Lab
-All rights reserved.
+Copyright (c) 2023, QuaDBio Lab
 
 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are met:
@@ -26,4 +25,4 @@ DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
 SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

README.md

@@ -1,2 +1,2 @@
-# Single-cell data analysis template repository
-This contains the raw structure I usually use when doing single-cell data analysis. 
+# Analysis template repository
+This contains the raw structure I usually use when doing single-cell/spatial data analysis. 

analysis/ML-2023-08-09_sample_notebook.ipynb

@@ -0,0 +1,215 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Title of the Analysis\n",
+    "Short description of what is being done here. \n",
+    "\n",
+    "Changelog\n",
+    "- XXX. "
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "hidePrompt": true
+   },
+   "source": [
+    "## Preliminaries"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Dependecy notebooks"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Links to notebooks/scripts that this analysis depends on. "
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Library imports"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "`autoreload` to re-load packages. "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2021-05-31T09:25:02.307098Z",
+     "start_time": "2021-05-31T09:25:02.291254Z"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "%load_ext autoreload\n",
+    "%autoreload 2"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "The actual imports. "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2021-05-31T09:25:05.984402Z",
+     "start_time": "2021-05-31T09:25:02.309195Z"
+    },
+    "hidePrompt": true
+   },
+   "outputs": [],
+   "source": [
+    "# import standard packages\n",
+    "import numpy as np\n",
+    "import pandas as pd \n",
+    "\n",
+    "import matplotlib.pyplot as plt\n",
+    "import seaborn as sns\n",
+    "\n",
+    "import sys\n",
+    "\n",
+    "# import single-cell packages\n",
+    "import scanpy as sc\n",
+    "\n",
+    "sys.path.extend([\"../\"])\n",
+    "from paths import DATA_DIR, FIG_DIR, CODE_DIR"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Print package versions. "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Running Scanpy 1.9.3, on 2023-08-09 11:52.\n"
+     ]
+    }
+   ],
+   "source": [
+    "sc.logging.print_version_and_date()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### General settings"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "sc.settings.figdir = str(FIG_DIR)\n",
+    "sc.settings.set_figure_params(dpi=100, dpi_save=300, frameon=False)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Function definitions"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Any utility functions you may need in this notebook go here. "
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Data loading"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Main analysis"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "py310",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.12"
+  },
+  "toc": {
+   "base_numbering": 1,
+   "nav_menu": {},
+   "number_sections": true,
+   "sideBar": true,
+   "skip_h1_title": false,
+   "title_cell": "Table of Contents",
+   "title_sidebar": "Contents",
+   "toc_cell": false,
+   "toc_position": {
+    "height": "calc(100% - 180px)",
+    "left": "10px",
+    "top": "150px",
+    "width": "288px"
+   },
+   "toc_section_display": true,
+   "toc_window_display": true
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}