deploy: ef4c415

sarajimenez · Nov 7, 2024 · 0b98fa3 · 0b98fa3
1 parent e9f1447
commit 0b98fa3
Show file tree

Hide file tree

Showing 72 changed files with 1,579 additions and 4,604 deletions.
diff --git a/_images/0485292fff5cb7ca4b68477fbc19c3e165f2c1494107cf364472338ece5cc996.png b/_images/0485292fff5cb7ca4b68477fbc19c3e165f2c1494107cf364472338ece5cc996.png
diff --git a/_images/083ec6fb89fa7156b8f10e1e4eee3be0f26550b5dcee02855ba28df8cab4b16f.png b/_images/083ec6fb89fa7156b8f10e1e4eee3be0f26550b5dcee02855ba28df8cab4b16f.png
diff --git a/_images/0c844084a96173d9ed9f2dc39fc8e1d5cf595e1e96238c6d7530d1dfe601c817.png b/_images/0c844084a96173d9ed9f2dc39fc8e1d5cf595e1e96238c6d7530d1dfe601c817.png
diff --git a/_images/12b41905ce7728b81ca8401e32a9269bb0cbe3adbaecb193c56f04392d190a72.png b/_images/12b41905ce7728b81ca8401e32a9269bb0cbe3adbaecb193c56f04392d190a72.png
diff --git a/_images/1449f2c05b547cd4f44669567d05d89595789372d4918407adeb6270b1257c4b.png b/_images/1449f2c05b547cd4f44669567d05d89595789372d4918407adeb6270b1257c4b.png
diff --git a/_images/1aeae91f8421b98f4333bae52d463315dee39cfb08d3e5ac04686399e2bf5b4d.png b/_images/1aeae91f8421b98f4333bae52d463315dee39cfb08d3e5ac04686399e2bf5b4d.png
diff --git a/_images/1bb6de518dac06beb20e4f02daa466602cc4fd8d3faca8437a6a3bcef4a0ec09.png b/_images/1bb6de518dac06beb20e4f02daa466602cc4fd8d3faca8437a6a3bcef4a0ec09.png
diff --git a/_images/1d066efd7f12e2766f84d953f9fec417e893b7b7fe69b6dbbb6e8ed31011d3bf.png b/_images/1d066efd7f12e2766f84d953f9fec417e893b7b7fe69b6dbbb6e8ed31011d3bf.png
diff --git a/_images/222b621beb4757907a67374af166ac328aac0de57dc6e0b4aae2cb4ae6af389f.png b/_images/222b621beb4757907a67374af166ac328aac0de57dc6e0b4aae2cb4ae6af389f.png
diff --git a/_images/241c9d0ab6943943fa3750153398225035606066e28ff99bbf329949a3ead0a2.png b/_images/241c9d0ab6943943fa3750153398225035606066e28ff99bbf329949a3ead0a2.png
diff --git a/_images/27ce52a58c2a0f764521c66ab92b13e299ec60193045c54dbb5700bfce153667.png b/_images/27ce52a58c2a0f764521c66ab92b13e299ec60193045c54dbb5700bfce153667.png
diff --git a/_images/29e927b5c425529eab774093f6a8f9dba034e7220af62cd3bf6cefda1bef6f83.png b/_images/29e927b5c425529eab774093f6a8f9dba034e7220af62cd3bf6cefda1bef6f83.png
diff --git a/_images/2cbd42d3fb1915d43b1d789f717ba80bc9d6a1680180c711f882fa2821162d6c.png b/_images/2cbd42d3fb1915d43b1d789f717ba80bc9d6a1680180c711f882fa2821162d6c.png
diff --git a/_images/2d18ee0ddf8e2f186318d67d79c1cb375016f612dab3d650c7600a42a824fa20.png b/_images/2d18ee0ddf8e2f186318d67d79c1cb375016f612dab3d650c7600a42a824fa20.png
diff --git a/_images/321219898f58495b6c4001aa4c25f4be614f7b18b6a6f6312c188595c7176977.png b/_images/321219898f58495b6c4001aa4c25f4be614f7b18b6a6f6312c188595c7176977.png
diff --git a/_images/342411c0bbfd7f2dae69a387f1cdbb350e26b028a9e46db54f8f354f2bc281c6.png b/_images/342411c0bbfd7f2dae69a387f1cdbb350e26b028a9e46db54f8f354f2bc281c6.png
diff --git a/_images/36ceaea67690cdff3ea09e608bba60ea9f1b02632108ab63ca16bd94e84621da.png b/_images/36ceaea67690cdff3ea09e608bba60ea9f1b02632108ab63ca16bd94e84621da.png
diff --git a/_images/38ba2b6b4eb5e08c76b8957443dd8530726de0c879aadea11896701e79c1e23e.png b/_images/38ba2b6b4eb5e08c76b8957443dd8530726de0c879aadea11896701e79c1e23e.png
diff --git a/_images/3d7e7c30082eec2eab8c11b6fa53b8ff28075a9192e9aa70e7b35daaf5b38a25.png b/_images/3d7e7c30082eec2eab8c11b6fa53b8ff28075a9192e9aa70e7b35daaf5b38a25.png
diff --git a/_images/3db433cee5ba75c11caf35483c3c79004e9629a38d7f3ddb91a64ce9514ba49f.png b/_images/3db433cee5ba75c11caf35483c3c79004e9629a38d7f3ddb91a64ce9514ba49f.png
diff --git a/_images/3f70383f277e102a33c0a5efeb3e1b346a5f5065b9d59cea300b8ec60fc32ca7.png b/_images/3f70383f277e102a33c0a5efeb3e1b346a5f5065b9d59cea300b8ec60fc32ca7.png
diff --git a/_images/3f78b0742c64e8048de387a0c82d45e4d44279eb152385221e2738ab501cfd77.png b/_images/3f78b0742c64e8048de387a0c82d45e4d44279eb152385221e2738ab501cfd77.png
diff --git a/_images/4367ed362055666ec8ddeb8497906bc3769604b2a6d3f15e503d580466dbd09b.png b/_images/4367ed362055666ec8ddeb8497906bc3769604b2a6d3f15e503d580466dbd09b.png
diff --git a/_images/466677740458c89dda010cfe97418b6ad7ab263428e3dd13d44dd58e25400a06.png b/_images/466677740458c89dda010cfe97418b6ad7ab263428e3dd13d44dd58e25400a06.png
diff --git a/_images/48a1f37dfa496fd93405f71c800079c64b8f43a48a513f3e875097998ff19174.png b/_images/48a1f37dfa496fd93405f71c800079c64b8f43a48a513f3e875097998ff19174.png
diff --git a/_images/4cbf4c8e9d4c8b6775bf1ad563f49b812e05f06697586ff71c7484c5b26591da.png b/_images/4cbf4c8e9d4c8b6775bf1ad563f49b812e05f06697586ff71c7484c5b26591da.png
diff --git a/_images/4f4425c058728113cd0e14efd200cf717d367ebb761f7194eb690cfb3336279b.png b/_images/4f4425c058728113cd0e14efd200cf717d367ebb761f7194eb690cfb3336279b.png
diff --git a/_images/642368f2f0211f0cdf5001a8bdbe36e01e04bb61e7b1f3e4204ef6be66df3b1b.png b/_images/642368f2f0211f0cdf5001a8bdbe36e01e04bb61e7b1f3e4204ef6be66df3b1b.png
diff --git a/_images/67fdea94117f20088e0856f020bbe1c0365931941ecc7f8394588053a607bf1e.png b/_images/67fdea94117f20088e0856f020bbe1c0365931941ecc7f8394588053a607bf1e.png
diff --git a/_images/697d321626cdf000e8e7ddc617f814673cd3b9fdc33746484721333d39bd55ff.png b/_images/697d321626cdf000e8e7ddc617f814673cd3b9fdc33746484721333d39bd55ff.png
diff --git a/_images/772957f77d4d24a4f3d7b13442dd3787480aa7e03c1e7640d68ec0239553d2de.png b/_images/772957f77d4d24a4f3d7b13442dd3787480aa7e03c1e7640d68ec0239553d2de.png
diff --git a/_images/78440b84997d129ce17460b90cae0153eb3c1ae034ff842df08afc89251edffa.png b/_images/78440b84997d129ce17460b90cae0153eb3c1ae034ff842df08afc89251edffa.png
diff --git a/_images/8907f09cff3a56e28d9f7488f0e1b3ae1fff0a4d599331a186dd15e45060ff2b.png b/_images/8907f09cff3a56e28d9f7488f0e1b3ae1fff0a4d599331a186dd15e45060ff2b.png
diff --git a/_images/8c88a2bf8b23e6760c40f4b71a1510188189a4f2a4be075c1ba482a52a1b6218.png b/_images/8c88a2bf8b23e6760c40f4b71a1510188189a4f2a4be075c1ba482a52a1b6218.png
diff --git a/_images/8ffd9ef29acd2bb3dedc908da532eee44d5a4b7b362eb5eb94f3854e5342bf38.png b/_images/8ffd9ef29acd2bb3dedc908da532eee44d5a4b7b362eb5eb94f3854e5342bf38.png
diff --git a/_images/90fa049c052667c291669e4011322722d14a71ebbaa84685f19714073adc556d.png b/_images/90fa049c052667c291669e4011322722d14a71ebbaa84685f19714073adc556d.png
diff --git a/_images/92bc5f7a1d43176648fe8e05be172d2efd1d6be3d8542edff92d37220e771970.png b/_images/92bc5f7a1d43176648fe8e05be172d2efd1d6be3d8542edff92d37220e771970.png
diff --git a/_images/a02860324cd66e00272ebd249d645319456252dc82c47543ff200a3e7658e87e.png b/_images/a02860324cd66e00272ebd249d645319456252dc82c47543ff200a3e7658e87e.png
diff --git a/_images/a04ea7179f6706d17d52752db6f823c11b1b4275472e42540085995322f3d181.png b/_images/a04ea7179f6706d17d52752db6f823c11b1b4275472e42540085995322f3d181.png
diff --git a/_images/a734d77da9e2608098b2ebcf3ec8c1f63fd389165023640c6546efa0dd4efb43.png b/_images/a734d77da9e2608098b2ebcf3ec8c1f63fd389165023640c6546efa0dd4efb43.png
diff --git a/_images/a89a7408d5603e7c635315a097408e7a29a5687e5173d12de3b9fed04097df51.png b/_images/a89a7408d5603e7c635315a097408e7a29a5687e5173d12de3b9fed04097df51.png
diff --git a/_images/afb5913d3f2c1fde1353f5b36a3436d83ea229cbb5c111563552495dd392375c.png b/_images/afb5913d3f2c1fde1353f5b36a3436d83ea229cbb5c111563552495dd392375c.png
diff --git a/_images/b191f6e12a863550e0643da2ae5998f817de5dc913471a0d200ddc0351a61e0c.png b/_images/b191f6e12a863550e0643da2ae5998f817de5dc913471a0d200ddc0351a61e0c.png
diff --git a/_images/b63cf419bdd29f9271eb4aeb10952ff871e6c49b977bc87d114a78c96ea57704.png b/_images/b63cf419bdd29f9271eb4aeb10952ff871e6c49b977bc87d114a78c96ea57704.png
diff --git a/_images/be9e7eb3aac4e7efb0ee2229a9fc71bdaf79e6dc3c8f3cf0af635e0cb18c4f9f.png b/_images/be9e7eb3aac4e7efb0ee2229a9fc71bdaf79e6dc3c8f3cf0af635e0cb18c4f9f.png
diff --git a/_images/c358c98249009cb20556db25859e2bad246ea8df64e302540f2164e189addf99.png b/_images/c358c98249009cb20556db25859e2bad246ea8df64e302540f2164e189addf99.png
diff --git a/_images/c63b43877c5aceecb42ff141fb31634215bb124d81a3fa8d59b923d175e5cc24.png b/_images/c63b43877c5aceecb42ff141fb31634215bb124d81a3fa8d59b923d175e5cc24.png
diff --git a/_images/c95d5f6a41e4581f83acddcb48fd77752761ef94f7cb34b79fe08aca4f3d2e19.png b/_images/c95d5f6a41e4581f83acddcb48fd77752761ef94f7cb34b79fe08aca4f3d2e19.png
diff --git a/_images/c965565215dfe90336123cb96ad0d7bf18fa2af73decbf32e26ef340986fbf2b.png b/_images/c965565215dfe90336123cb96ad0d7bf18fa2af73decbf32e26ef340986fbf2b.png
diff --git a/_images/dfa42fd68521fd203b5431d8c82e0658bf869aab8877f18d21c0355d0aeb51f7.png b/_images/dfa42fd68521fd203b5431d8c82e0658bf869aab8877f18d21c0355d0aeb51f7.png
diff --git a/_images/e221c4b6b221c5c5cde6eea5f11379c9808d6545ce2d67657352f626812dbb7a.png b/_images/e221c4b6b221c5c5cde6eea5f11379c9808d6545ce2d67657352f626812dbb7a.png
diff --git a/_images/e863bd4e12aff3e17405f0f1dcdb6e944966e9ed5014c652c821f2bde3e2f2b9.png b/_images/e863bd4e12aff3e17405f0f1dcdb6e944966e9ed5014c652c821f2bde3e2f2b9.png
diff --git a/_images/e95898b6861c0b940251f174b9228f7d7268f43a8ee4429068993416fdb6e29a.png b/_images/e95898b6861c0b940251f174b9228f7d7268f43a8ee4429068993416fdb6e29a.png
diff --git a/_images/e9be17bbd190abc3e09f36fae945acd6e4b4fa25622e557cd7a13656c3385b56.png b/_images/e9be17bbd190abc3e09f36fae945acd6e4b4fa25622e557cd7a13656c3385b56.png
diff --git a/_images/eefac8ca815f464e0164b3022128b143ab4dee4588e99c928163a3df9bdf70a9.png b/_images/eefac8ca815f464e0164b3022128b143ab4dee4588e99c928163a3df9bdf70a9.png
diff --git a/_images/ef7ef7bd6cf1cced5972577aaf1cf61791168b8635e676972fc1f309401d0630.png b/_images/ef7ef7bd6cf1cced5972577aaf1cf61791168b8635e676972fc1f309401d0630.png
diff --git a/_images/f3f8ff2f5d6cb3df43a05962868d3b7e2f6faec18acad4d2950dbac7ea63196b.png b/_images/f3f8ff2f5d6cb3df43a05962868d3b7e2f6faec18acad4d2950dbac7ea63196b.png
diff --git a/_images/f90854b110b7a14132ce77f55dc809d5e8bffd158d073b2704115745d9ece7a7.png b/_images/f90854b110b7a14132ce77f55dc809d5e8bffd158d073b2704115745d9ece7a7.png
diff --git a/_sources/session-1.ipynb b/_sources/session-1.ipynb
@@ -38,16 +38,6 @@
     "Install all packages for the tutorial"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "fa6fa7cf",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "!pip install scanpy scrublet"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": 37,
@@ -68,75 +58,6 @@
     "import scrublet as scr\n"
    ]
   },
-  {
-   "attachments": {},
-   "cell_type": "markdown",
-   "id": "a3a2cf51",
-   "metadata": {},
-   "source": [
-    "# Set project file paths  \n",
-    "\n",
-    "Let us set up the connection with Google Drive"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "16f798c5",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "from google.colab import drive\n",
-    "drive.mount('/content/drive')"
-   ]
-  },
-  {
-   "attachments": {},
-   "cell_type": "markdown",
-   "id": "85a97d70",
-   "metadata": {},
-   "source": [
-    "We set up the file paths to the respective directories."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "205a5ade",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "file_path = '/content/drive/My Drive/' #this is the file path to your google drive (main directory)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "8521c899",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "os.listdir(file_path) #shows all files in file_path"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "ec00f7a2",
-   "metadata": {},
-   "source": [
-    "The data directory contains all processed data and `anndata` files. "
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "1dd6302a",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "data_dir = file_path + 'GSCN_workshop_2024/Data/' "
-   ]
-  },
   {
    "cell_type": "markdown",
    "id": "2970f5d6",