run notebooks

bfurtwa · May 3, 2021 · 29a1e5a · 29a1e5a
1 parent 63e3486
commit 29a1e5a
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Showing 8 changed files with 511 additions and 474 deletions.
diff --git a/Schoof_et_al/code/300ms.ipynb b/Schoof_et_al/code/300ms.ipynb
diff --git a/Schoof_et_al/code/300ms_vs_500ms.ipynb b/Schoof_et_al/code/300ms_vs_500ms.ipynb
@@ -9,7 +9,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 394,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -27,7 +27,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 395,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -39,7 +39,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 396,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -48,7 +48,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 397,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -59,7 +59,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 398,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -70,7 +70,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 399,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -86,7 +86,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 400,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [
     {
@@ -124,7 +124,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 401,
+   "execution_count": 8,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -138,7 +138,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 402,
+   "execution_count": 9,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -148,7 +148,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 403,
+   "execution_count": 10,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -171,7 +171,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 404,
+   "execution_count": 11,
    "metadata": {},
    "outputs": [
     {
@@ -204,7 +204,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 405,
+   "execution_count": 12,
    "metadata": {},
    "outputs": [
     {
@@ -230,7 +230,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 406,
+   "execution_count": 13,
    "metadata": {},
    "outputs": [
     {
@@ -288,7 +288,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 407,
+   "execution_count": 14,
    "metadata": {},
    "outputs": [
     {
@@ -310,7 +310,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 408,
+   "execution_count": 15,
    "metadata": {},
    "outputs": [
     {
@@ -368,7 +368,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 409,
+   "execution_count": 16,
    "metadata": {},
    "outputs": [
     {
@@ -390,7 +390,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 410,
+   "execution_count": 17,
    "metadata": {},
    "outputs": [
     {
@@ -448,7 +448,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 411,
+   "execution_count": 18,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -468,7 +468,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 412,
+   "execution_count": 19,
    "metadata": {},
    "outputs": [
     {
@@ -522,7 +522,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 413,
+   "execution_count": 20,
    "metadata": {},
    "outputs": [
     {
@@ -567,7 +567,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 414,
+   "execution_count": 21,
    "metadata": {},
    "outputs": [
     {
@@ -584,15 +584,15 @@
      "text": [
       "computing PCA\n",
       "    with n_comps=50\n",
-      "    finished (0:00:03)\n",
+      "    finished (0:00:01)\n",
       "computing PCA\n",
       "    with n_comps=50\n",
-      "    finished (0:00:02)\n",
+      "    finished (0:00:00)\n",
       "computing neighbors\n",
       "    using 'X_pca' with n_pcs = 50\n",
       "    finished: added to `.uns['neighbors']`\n",
       "    `.obsp['distances']`, distances for each pair of neighbors\n",
-      "    `.obsp['connectivities']`, weighted adjacency matrix (0:00:00)\n",
+      "    `.obsp['connectivities']`, weighted adjacency matrix (0:00:03)\n",
       "computing neighbors\n",
       "    using 'X_pca' with n_pcs = 50\n",
       "    finished: added to `.uns['neighbors']`\n",
@@ -633,7 +633,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 415,
+   "execution_count": 22,
    "metadata": {},
    "outputs": [
     {
@@ -671,7 +671,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 416,
+   "execution_count": 23,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -685,7 +685,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 417,
+   "execution_count": 24,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -695,7 +695,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 418,
+   "execution_count": 25,
    "metadata": {},
    "outputs": [
     {
@@ -715,7 +715,7 @@
        "Name: gene, Length: 1270, dtype: object"
       ]
      },
-     "execution_count": 418,
+     "execution_count": 25,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -729,7 +729,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 419,
+   "execution_count": 26,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -739,7 +739,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 420,
+   "execution_count": 27,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -762,7 +762,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 421,
+   "execution_count": 28,
    "metadata": {},
    "outputs": [
     {
@@ -794,7 +794,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 422,
+   "execution_count": 29,
    "metadata": {},
    "outputs": [
     {
@@ -820,7 +820,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 423,
+   "execution_count": 30,
    "metadata": {},
    "outputs": [
     {
@@ -829,7 +829,7 @@
        "Text(0.5, -0.06, 'log2FC single-cells')"
       ]
      },
-     "execution_count": 423,
+     "execution_count": 30,
      "metadata": {},
      "output_type": "execute_result"
     },
@@ -878,7 +878,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 424,
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 31,
    "metadata": {},
    "outputs": [
     {
@@ -887,7 +894,7 @@
        "0"
       ]
      },
-     "execution_count": 424,
+     "execution_count": 31,
      "metadata": {},
      "output_type": "execute_result"
     }

diff --git a/Schoof_et_al/code/500ms.ipynb b/Schoof_et_al/code/500ms.ipynb
diff --git a/Schoof_et_al/code/booster_only.ipynb b/Schoof_et_al/code/booster_only.ipynb
diff --git a/Schoof_et_al/code/bulk.ipynb b/Schoof_et_al/code/bulk.ipynb