Merge branch 'documentation' of github.com:pachterlab/voyager into do…

…cumentation
pachterlab · May 15, 2024 · d812496 · d812496
2 parents 24faf06 + 02175f0
commit d812496
Show file tree

Hide file tree

Showing 32 changed files with 1,751 additions and 39,665 deletions.
diff --git a/vignettes/bivariate.ipynb b/vignettes/bivariate.ipynb
diff --git a/vignettes/create_sfe.ipynb b/vignettes/create_sfe.ipynb
diff --git a/vignettes/create_sfe_v2.ipynb b/vignettes/create_sfe_v2.ipynb
diff --git a/vignettes/localc.ipynb b/vignettes/localc.ipynb
diff --git a/vignettes/multispati.ipynb b/vignettes/multispati.ipynb
diff --git a/vignettes/nonspatial.ipynb b/vignettes/nonspatial.ipynb
diff --git a/vignettes/preprocess_10xv3.ipynb b/vignettes/preprocess_10xv3.ipynb
diff --git a/vignettes/preprocess_atac.ipynb b/vignettes/preprocess_atac.ipynb
diff --git a/vignettes/preprocess_clicktag.ipynb b/vignettes/preprocess_clicktag.ipynb
diff --git a/vignettes/preprocess_crispr.ipynb b/vignettes/preprocess_crispr.ipynb
diff --git a/vignettes/preprocess_multiome.ipynb b/vignettes/preprocess_multiome.ipynb
diff --git a/vignettes/preprocess_nuclei.ipynb b/vignettes/preprocess_nuclei.ipynb
diff --git a/vignettes/preprocess_splitseq.ipynb b/vignettes/preprocess_splitseq.ipynb
diff --git a/vignettes/preprocess_visium.ipynb b/vignettes/preprocess_visium.ipynb
diff --git a/vignettes/sfemethod.ipynb b/vignettes/sfemethod.ipynb
diff --git a/vignettes/variogram.ipynb b/vignettes/variogram.ipynb
diff --git a/vignettes/vig10_10x_nuclei.ipynb b/vignettes/vig10_10x_nuclei.ipynb
diff --git a/vignettes/vig11_clicktags.ipynb b/vignettes/vig11_clicktags.ipynb
diff --git a/vignettes/vig12_crispr.ipynb b/vignettes/vig12_crispr.ipynb
diff --git a/vignettes/vig13_10xatac.ipynb b/vignettes/vig13_10xatac.ipynb
@@ -2,31 +2,7 @@
  "cells": [
   {
    "cell_type": "raw",
-<<<<<<< HEAD
-<<<<<<< HEAD
-<<<<<<< HEAD
-   "id": "dd4f2f31",
-||||||| fa5abb84
-   "id": "b0a7963d",
-=======
-   "id": "e91e6957",
->>>>>>> documentation-devel
-||||||| 7e3277eb
-   "id": "e91e6957",
-=======
-   "id": "7529388d",
->>>>>>> documentation-devel
-||||||| 971bf77c
-<<<<<<< HEAD
-   "id": "dd4f2f31",
-||||||| fa5abb84
-   "id": "b0a7963d",
-=======
-   "id": "e91e6957",
->>>>>>> documentation-devel
-=======
-   "id": "c44ea834",
->>>>>>> e1d793125c0aeb7e34aca09298b9c5b44973e4b3
+   "id": "d3e6f64c",
    "metadata": {},
    "source": [
     "---\n",
@@ -50,31 +26,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-<<<<<<< HEAD
-<<<<<<< HEAD
-<<<<<<< HEAD
-   "id": "85ec514d",
-||||||| fa5abb84
-   "id": "09d8e82c",
-=======
-   "id": "ed19ee41",
->>>>>>> documentation-devel
-||||||| 7e3277eb
-   "id": "ed19ee41",
-=======
-   "id": "3f954c85",
->>>>>>> documentation-devel
-||||||| 971bf77c
-<<<<<<< HEAD
-   "id": "85ec514d",
-||||||| fa5abb84
-   "id": "09d8e82c",
-=======
-   "id": "ed19ee41",
->>>>>>> documentation-devel
-=======
-   "id": "9889af05",
->>>>>>> e1d793125c0aeb7e34aca09298b9c5b44973e4b3
+   "id": "29c5db40",
    "metadata": {
     "tags": [
      "remove_cell"
@@ -91,31 +43,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-<<<<<<< HEAD
-<<<<<<< HEAD
-<<<<<<< HEAD
-   "id": "058c3c38",
-||||||| fa5abb84
-   "id": "564cf943",
-=======
-   "id": "3bb4834c",
->>>>>>> documentation-devel
-||||||| 7e3277eb
-   "id": "3bb4834c",
-=======
-   "id": "cc15d387",
->>>>>>> documentation-devel
-||||||| 971bf77c
-<<<<<<< HEAD
-   "id": "058c3c38",
-||||||| fa5abb84
-   "id": "564cf943",
-=======
-   "id": "3bb4834c",
->>>>>>> documentation-devel
-=======
-   "id": "3b18557d",
->>>>>>> e1d793125c0aeb7e34aca09298b9c5b44973e4b3
+   "id": "69ef8669",
    "metadata": {
     "eval": false,
     "tags": [
@@ -150,31 +78,7 @@
   },
   {
    "cell_type": "markdown",
-<<<<<<< HEAD
-<<<<<<< HEAD
-<<<<<<< HEAD
-   "id": "e3feb65c",
-||||||| fa5abb84
-   "id": "7e1441f8",
-=======
-   "id": "95fc9b16",
->>>>>>> documentation-devel
-||||||| 7e3277eb
-   "id": "95fc9b16",
-=======
-   "id": "5478e541",
->>>>>>> documentation-devel
-||||||| 971bf77c
-<<<<<<< HEAD
-   "id": "e3feb65c",
-||||||| fa5abb84
-   "id": "7e1441f8",
-=======
-   "id": "95fc9b16",
->>>>>>> documentation-devel
-=======
-   "id": "b76b0e18",
->>>>>>> e1d793125c0aeb7e34aca09298b9c5b44973e4b3
+   "id": "c7d6dd0f",
    "metadata": {},
    "source": [
     "# Introduction\n",
@@ -184,31 +88,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-<<<<<<< HEAD
-<<<<<<< HEAD
-<<<<<<< HEAD
-   "id": "0ebbaf1c",
-||||||| fa5abb84
-   "id": "b997d83b",
-=======
-   "id": "6877f6c5",
->>>>>>> documentation-devel
-||||||| 7e3277eb
-   "id": "6877f6c5",
-=======
-   "id": "2b37174a",
->>>>>>> documentation-devel
-||||||| 971bf77c
-<<<<<<< HEAD
-   "id": "0ebbaf1c",
-||||||| fa5abb84
-   "id": "b997d83b",
-=======
-   "id": "6877f6c5",
->>>>>>> documentation-devel
-=======
-   "id": "4b62ca22",
->>>>>>> e1d793125c0aeb7e34aca09298b9c5b44973e4b3
+   "id": "983b91a8",
    "metadata": {
     "message": false
    },
@@ -229,64 +109,13 @@
   {
    "cell_type": "code",
    "execution_count": null,
-<<<<<<< HEAD
-<<<<<<< HEAD
-<<<<<<< HEAD
-   "id": "e25d0c5d",
-||||||| 971bf77c
-<<<<<<< HEAD
-   "id": "e25d0c5d",
-=======
-   "id": "9c979425",
->>>>>>> e1d793125c0aeb7e34aca09298b9c5b44973e4b3
+   "id": "5e1a5a4e",
    "metadata": {
     "message": true,
     "tags": [
      "remove_output"
     ]
    },
-<<<<<<< HEAD
-||||||| fa5abb84
-   "id": "ab78761d",
-   "metadata": {
-    "message": false,
-    "name": "dwnld",
-    "tags": [
-     "remove_output"
-    ]
-   },
-=======
-   "id": "3d614589",
-   "metadata": {},
->>>>>>> documentation-devel
-||||||| 7e3277eb
-   "id": "3d614589",
-   "metadata": {},
-=======
-   "id": "a70cbd72",
-   "metadata": {
-    "message": true,
-    "tags": [
-     "remove_output"
-    ]
-   },
->>>>>>> documentation-devel
-||||||| 971bf77c
-||||||| fa5abb84
-   "id": "ab78761d",
-   "metadata": {
-    "message": false,
-    "name": "dwnld",
-    "tags": [
-     "remove_output"
-    ]
-   },
-=======
-   "id": "3d614589",
-   "metadata": {},
->>>>>>> documentation-devel
-=======
->>>>>>> e1d793125c0aeb7e34aca09298b9c5b44973e4b3
    "outputs": [],
    "source": [
     "if (!file.exists(\"10xatac.rds\"))\n",
@@ -297,31 +126,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-<<<<<<< HEAD
-<<<<<<< HEAD
-<<<<<<< HEAD
-   "id": "14826478",
-||||||| fa5abb84
-   "id": "8cf35f1e",
-=======
-   "id": "5d9e7977",
->>>>>>> documentation-devel
-||||||| 7e3277eb
-   "id": "5d9e7977",
-=======
-   "id": "2dcbb348",
->>>>>>> documentation-devel
-||||||| 971bf77c
-<<<<<<< HEAD
-   "id": "14826478",
-||||||| fa5abb84
-   "id": "8cf35f1e",
-=======
-   "id": "5d9e7977",
->>>>>>> documentation-devel
-=======
-   "id": "268566ca",
->>>>>>> e1d793125c0aeb7e34aca09298b9c5b44973e4b3
+   "id": "05ce1347",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -332,31 +137,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-<<<<<<< HEAD
-<<<<<<< HEAD
-<<<<<<< HEAD
-   "id": "63f68344",
-||||||| fa5abb84
-   "id": "34e4126e",
-=======
-   "id": "c7bcfbb0",
->>>>>>> documentation-devel
-||||||| 7e3277eb
-   "id": "c7bcfbb0",
-=======
-   "id": "c8b7d785",
->>>>>>> documentation-devel
-||||||| 971bf77c
-<<<<<<< HEAD
-   "id": "63f68344",
-||||||| fa5abb84
-   "id": "34e4126e",
-=======
-   "id": "c7bcfbb0",
->>>>>>> documentation-devel
-=======
-   "id": "185b6235",
->>>>>>> e1d793125c0aeb7e34aca09298b9c5b44973e4b3
+   "id": "d176b932",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -367,31 +148,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-<<<<<<< HEAD
-<<<<<<< HEAD
-<<<<<<< HEAD
-   "id": "c2bf812d",
-||||||| fa5abb84
-   "id": "6f2463b6",
-=======
-   "id": "194c5b71",
->>>>>>> documentation-devel
-||||||| 7e3277eb
-   "id": "194c5b71",
-=======
-   "id": "0b4076c9",
->>>>>>> documentation-devel
-||||||| 971bf77c
-<<<<<<< HEAD
-   "id": "c2bf812d",
-||||||| fa5abb84
-   "id": "6f2463b6",
-=======
-   "id": "194c5b71",
->>>>>>> documentation-devel
-=======
-   "id": "7970b3dc",
->>>>>>> e1d793125c0aeb7e34aca09298b9c5b44973e4b3
+   "id": "63ac0891",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -402,31 +159,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-<<<<<<< HEAD
-<<<<<<< HEAD
-<<<<<<< HEAD
-   "id": "16476da3",
-||||||| fa5abb84
-   "id": "28c399c5",
-=======
-   "id": "96d83612",
->>>>>>> documentation-devel
-||||||| 7e3277eb
-   "id": "96d83612",
-=======
-   "id": "44154bb4",
->>>>>>> documentation-devel
-||||||| 971bf77c
-<<<<<<< HEAD
-   "id": "16476da3",
-||||||| fa5abb84
-   "id": "28c399c5",
-=======
-   "id": "96d83612",
->>>>>>> documentation-devel
-=======
-   "id": "5a798106",
->>>>>>> e1d793125c0aeb7e34aca09298b9c5b44973e4b3
+   "id": "4fba447e",
    "metadata": {
     "name": "subset-qc"
    },
@@ -441,31 +174,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-<<<<<<< HEAD
-<<<<<<< HEAD
-<<<<<<< HEAD
-   "id": "9b1bc190",
-||||||| fa5abb84
-   "id": "bd3414eb",
-=======
-   "id": "9f9ef222",
->>>>>>> documentation-devel
-||||||| 7e3277eb
-   "id": "9f9ef222",
-=======
-   "id": "fadf33b7",
->>>>>>> documentation-devel
-||||||| 971bf77c
-<<<<<<< HEAD
-   "id": "9b1bc190",
-||||||| fa5abb84
-   "id": "bd3414eb",
-=======
-   "id": "9f9ef222",
->>>>>>> documentation-devel
-=======
-   "id": "88274144",
->>>>>>> e1d793125c0aeb7e34aca09298b9c5b44973e4b3
+   "id": "6961337c",
    "metadata": {},
    "outputs": [],
    "source": [