✨ add other notebooks (scripts)

RasmussenLab · May 29, 2024 · e4a244e · e4a244e
1 parent 43b3539
commit e4a244e
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Showing 7 changed files with 17 additions and 8 deletions.
diff --git a/conf.py b/conf.py
@@ -16,6 +16,7 @@
 copyright = '2022, Marc Pielies Avelli'
 author = 'Marc Pielies Avelli'
 version = '2024.05.29'
+release = '2024.05.29'
 
 # -- General configuration ---------------------------------------------------
 
@@ -70,7 +71,7 @@
 # a list of builtin themes.
 # See:
 # https://github.com/executablebooks/MyST-NB/blob/master/docs/conf.py
-html_title = ""
+html_title = "CLASTER"
 html_theme = "sphinx_book_theme"
 # html_logo = "_static/logo-wide.svg"
 # html_favicon = "_static/logo-square.svg"

diff --git a/index.rst b/index.rst
@@ -13,3 +13,11 @@ Modeling nascent RNA transcription from chromatin landscape and structure
 
     scripts/0_Tutorial.ipynb
 
+.. toctree::
+    :maxdepth: 2
+    :caption: Scripts:
+
+    scripts/1_Data_obtention.ipynb
+    scripts/2_Run_CLASTER.ipynb
+    scripts/2b_Run_HyenaDNA_and_Enformer.ipynb
+    scripts/3_Data_analysis.ipynb
diff --git a/scripts/0_Tutorial.ipynb b/scripts/0_Tutorial.ipynb
@@ -1635,7 +1635,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.9"
+   "version": "3.undefined.undefined"
   },
   "orig_nbformat": 4,
   "vscode": {

diff --git a/scripts/1_Data_obtention.ipynb b/scripts/1_Data_obtention.ipynb
@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# <center> 1. DATA OBTENTION & PREPROCESSING <center>\n",
+    "# 1. DATA OBTENTION & PREPROCESSING\n",
     "\n",
     "Hi!\n",
     "This notebook is a guide to obtain and preprocess the data used to train and test CLASTER. It is meant to be run sequentially, i.e. one cell after the other, and it mainly contains:\n",
@@ -18,7 +18,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Before we start ...\n",
+    "## Before we start ...\n",
     "\n",
     "A) It would be highly recommendable to create an environment for this project. The python package EIR, which is the core framework used to build, train and test CLASTER, will need python >= 3.11. If you have anaconda, it can be done as follows from the terminal:\n",
     "\n",
@@ -69,7 +69,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# 1. Data obtention"
+    "## 1. Data obtention"
    ]
   },
   {

diff --git a/scripts/2_Run_CLASTER.ipynb b/scripts/2_Run_CLASTER.ipynb
@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# <center> 2. CREATE & RUN CLASTER <center>"
+    "# 2. CREATE & RUN CLASTER"
    ]
   },
   {

diff --git a/scripts/2b_Run_HyenaDNA_and_Enformer.ipynb b/scripts/2b_Run_HyenaDNA_and_Enformer.ipynb
@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# <center> 2b. BENCHMARKING CLASTER WITH HYENA-DNA AND ENFORMER <center>"
+    "# 2b. BENCHMARKING CLASTER WITH HYENA-DNA AND ENFORMER"
    ]
   },
   {

diff --git a/scripts/3_Data_analysis.ipynb b/scripts/3_Data_analysis.ipynb
@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# <center> DATA ANALYSIS NOTEBOOK <center>\n",
+    "# DATA ANALYSIS NOTEBOOK\n",
     "\n",
     "This notebook was used to run the analyses and produce most of the images in the paper.\n",
     "\n",