Database / manifests /1d /zenodo__17871734.json
opsecsystems's picture
Scripts of 2026-09-30: 1 new block(s), 415 manifest(s), 0 removed
3303fc6 verified
Raw History Blame Contribute Delete
27.1 kB
{
"format": "oscr-script-manifest/1",
"repository": "zenodo:17871734",
"url": "https://doi.org/10.5281/Zenodo.17871734",
"host": "zenodo.org",
"commit": "",
"license": "MIT",
"license_confirmed_by": "license file LICENSE",
"redistribution": "yes",
"files": [
{
"path": "1.sc_snRNAseq_preprocessing/1-filtering.R",
"sha256": "c0130cfb16064872c4213c3878f43de3f14de4283ce2f14e76c682bc169e5eea",
"language": "R",
"lines": 359,
"truncated": false,
"block": 10,
"row": 18824
},
{
"path": "1.sc_snRNAseq_preprocessing/10_classification_malignant_normal.R",
"sha256": "b593b9199e777af0f144e4b6b8d3f5353ce6ebeb87d75b1cfcf3b97a16c624ff",
"language": "R",
"lines": 280,
"truncated": false,
"block": 10,
"row": 18749
},
{
"path": "1.sc_snRNAseq_preprocessing/2-Plots.R",
"sha256": "d8f2f2a7cafd35a9875304e48ea104bf7ae2ed43087c263da440516b6b38ccea",
"language": "R",
"lines": 64,
"truncated": false,
"block": 10,
"row": 18232
},
{
"path": "1.sc_snRNAseq_preprocessing/3a-infercnv_frozen_step1_part1.R",
"sha256": "0d4ee780913a4b5c23ccd83731e8dcd2dd4b078d02026b5ecd54034255c5a658",
"language": "R",
"lines": 165,
"truncated": false,
"block": 10,
"row": 18528
},
{
"path": "1.sc_snRNAseq_preprocessing/3b-infercnv_fresh_step1_part1.R",
"sha256": "b53af45d8dc29cb0d84727a582702eb38b34041976e9dabdf114d4b227d405fe",
"language": "R",
"lines": 131,
"truncated": false,
"block": 10,
"row": 18457
},
{
"path": "1.sc_snRNAseq_preprocessing/4a-infercnv_frozen_step2.R",
"sha256": "e7a4cae4397b669d0245439c5fa88d6e4b1ed103b4f70a929092a05e1bca652b",
"language": "R",
"lines": 102,
"truncated": false,
"block": 10,
"row": 18366
},
{
"path": "1.sc_snRNAseq_preprocessing/4b-infercnv_fresh_step2.R",
"sha256": "e9b0f0c6c99f9aa0eca3e60619993b7ba4c290e699514d0bd1ab0f3a6c593e16",
"language": "R",
"lines": 103,
"truncated": false,
"block": 10,
"row": 18361
},
{
"path": "1.sc_snRNAseq_preprocessing/5a-infercnv_frozen_step3.R",
"sha256": "7605180bad39eea5a96fbbe267d0003cb4e58ffc04af62bf213509dbfdcc0e77",
"language": "R",
"lines": 188,
"truncated": false,
"block": 10,
"row": 18567
},
{
"path": "1.sc_snRNAseq_preprocessing/5b-infercnv_fresh_step3.R",
"sha256": "5a2fa85d341a520fc1476004122dbefcfc58efdbc46ba9c01c2926935954c06d",
"language": "R",
"lines": 179,
"truncated": false,
"block": 10,
"row": 18557
},
{
"path": "1.sc_snRNAseq_preprocessing/6-prepare_nmf_counts.R",
"sha256": "7ea0cf2f0d07ea4eca72ad87401c73ecd43c7d674a7a2250355e300b8465f14c",
"language": "R",
"lines": 28,
"truncated": false,
"block": 10,
"row": 17918
},
{
"path": "1.sc_snRNAseq_preprocessing/6b-prepare_nmf_counts_fresh.R",
"sha256": "b6e21b224f5d3bacb7147b1e9d0e3795f7a33837f70728fec2ee33b42b9dbea7",
"language": "R",
"lines": 28,
"truncated": false,
"block": 10,
"row": 17917
},
{
"path": "1.sc_snRNAseq_preprocessing/7-NMF_rank-forO2.R",
"sha256": "e1c60b11f89daa0dec6820de7023f287672f31672a1ce1f99c1c45d951feaeb3",
"language": "R",
"lines": 81,
"truncated": false,
"block": 10,
"row": 18183
},
{
"path": "1.sc_snRNAseq_preprocessing/7b-NMF_rank-batch.sh",
"sha256": "7ab5bd19c23501e40c1d0231a52ac1e7c3f0ca65d9eb32408869149cd0cb578a",
"language": "Shell",
"lines": 16,
"truncated": false,
"block": 10,
"row": 19147
},
{
"path": "1.sc_snRNAseq_preprocessing/7c-NMF_terminal_code.sh",
"sha256": "336374aa9412d419e73f21aae6fad38f15c9f75ecdde3943256da056cd9a5924",
"language": "Shell",
"lines": 3,
"truncated": false,
"block": 10,
"row": 19011
},
{
"path": "1.sc_snRNAseq_preprocessing/8-NMF.Rmd",
"sha256": "9d429c38b3a4519123e71d066d02e5c3d2c601da27999c61e44a02b3f9a1b413",
"language": "R",
"lines": 945,
"truncated": false,
"block": 10,
"row": 18932
},
{
"path": "1.sc_snRNAseq_preprocessing/9_Cleanup_datasets.R",
"sha256": "0d93dfdbe2a9e696c6e76b7d2f9d64d5c936cfa7a097548fe2484e974ffa4d85",
"language": "R",
"lines": 248,
"truncated": false,
"block": 10,
"row": 18651
},
{
"path": "1.sc_snRNAseq_preprocessing/Oncoprint.R",
"sha256": "453aea0a941103fb7bd1547be38b54a7d14d75511cdc3ae56184b068438cd854",
"language": "R",
"lines": 630,
"truncated": false,
"block": 10,
"row": 18869
},
{
"path": "1.sc_snRNAseq_preprocessing/resources/Color_palette.R",
"sha256": "e7e55806d05ddc593ae2ae860e709b7fc973c63df729f6728a50b7d2b37b38d0",
"language": "R",
"lines": 78,
"truncated": false,
"block": 10,
"row": 18182
},
{
"path": "1.sc_snRNAseq_preprocessing/resources/NMF_helper_function.R",
"sha256": "db417371968fff7d4d47bc106bf71e942e12557f1c1b604eb5cc78ab7752f834",
"language": "R",
"lines": 239,
"truncated": false,
"block": 10,
"row": 18576
},
{
"path": "1.sc_snRNAseq_preprocessing/resources/Plot_style.R",
"sha256": "a43967d8ad5449e62fc0021b66ccbe5733b58f11f222fd5b7bd05f9346c048ba",
"language": "R",
"lines": 27,
"truncated": false,
"block": 10,
"row": 17962
},
{
"path": "1.sc_snRNAseq_preprocessing/resources/Plot_style_oncoplot.R",
"sha256": "ebe29b455a8b6924bbfdcc4630e489ccdfc37df5aa667f8fd136d2c003569b64",
"language": "R",
"lines": 112,
"truncated": false,
"block": 10,
"row": 18395
},
{
"path": "1.sc_snRNAseq_preprocessing/resources/Plot_style_v2.R",
"sha256": "85e0719f71c3718579659d4a448dfaa37d0573c67e080e22367b2c86b5d1c23b",
"language": "R",
"lines": 52,
"truncated": false,
"block": 10,
"row": 18221
},
{
"path": "1.sc_snRNAseq_preprocessing/resources/Plotting_helper_functions.R",
"sha256": "e0b894197dd0bc1d788a78c7c068c184b9594b9d7fcf43eb07ab1336634cb1ac",
"language": "R",
"lines": 608,
"truncated": false,
"block": 10,
"row": 18874
},
{
"path": "1.sc_snRNAseq_preprocessing/resources/common_stat_test.R",
"sha256": "bdd80425cafbb5342b1ed730eaeb2710975c54f8aba73d0b9b73a4cc628fff99",
"language": "R",
"lines": 15,
"truncated": false,
"block": 10,
"row": 17879
},
{
"path": "1.sc_snRNAseq_preprocessing/resources/functions.R",
"sha256": "ce065ae3f33997f6a0c50adc00b45e4a739887a385bbf1f4ba1d3ad6d2cc7f14",
"language": "R",
"lines": 12,
"truncated": false,
"block": 10,
"row": 17878
},
{
"path": "1.sc_snRNAseq_preprocessing/resources/inferCNV_helper_functions.R",
"sha256": "9bb3c991d50bac13ccc396e0488ccfb1a9e7b035e8f4ca7b59b9664dd0656eca",
"language": "R",
"lines": 659,
"truncated": false,
"block": 10,
"row": 18902
},
{
"path": "1.sc_snRNAseq_preprocessing/resources/plotutils.R",
"sha256": "12bec5da7492020e645bb3df17972ad0081092986dd227473c98a0430ba904d5",
"language": "R",
"lines": 238,
"truncated": false,
"block": 10,
"row": 18704
},
{
"path": "1.sc_snRNAseq_preprocessing/resources/single_cell_preprocessing_helper_functions.R",
"sha256": "5bff882ea9b8c0846a45f102451f2eab9a4d76ab15c22789511aba0544a9cd95",
"language": "R",
"lines": 1026,
"truncated": false,
"block": 10,
"row": 18933
},
{
"path": "1.sc_snRNAseq_preprocessing/resources/single_cell_preprocessing_helper_functions_CBJr.R",
"sha256": "1c033361ee7eb039c3a5bae660ca4bd396c226fcafd2723988e298f87505196c",
"language": "R",
"lines": 1284,
"truncated": false,
"block": 10,
"row": 18954
},
{
"path": "2.Plots/Figure1/1_ST_EPN_classification_malignant_normal_Fig1c.R",
"sha256": "07c496635732a953df86304712aa2bcdbd291f32bfbe40f2ad9ed267a6451207",
"language": "R",
"lines": 300,
"truncated": false,
"block": 10,
"row": 18769
},
{
"path": "2.Plots/Figure1/5_Pseudobulk_correlation_Fig1b.R",
"sha256": "2af97529f9f84023367a6999d36b5e04e8df5144df6ef0fd26807dce35c53007",
"language": "R",
"lines": 202,
"truncated": false,
"block": 10,
"row": 18572
},
{
"path": "2.Plots/Figure1/panel_c.R",
"sha256": "4331e79197cd152b26a8789383b77e3687d259d15b6ed09570d5ca89e656c589",
"language": "R",
"lines": 18,
"truncated": false,
"block": 10,
"row": 17890
},
{
"path": "2.Plots/Figure2/2_ST-EPN_malignant_Fig2.Rmd",
"sha256": "1aafe0bfd8bdf0c5800e910d22592cc85c4b86d2f02d2e0196551c23f2a3f54f",
"language": "R",
"lines": 909,
"truncated": false,
"block": 10,
"row": 18900
},
{
"path": "2.Plots/Figure2/3_heatmap_STEPN_NMF_genes_Fig2b.R",
"sha256": "690b6a860a0d99d67c594a13bd2e10c7c9dad091fa5a7432b31fb17dc3024821",
"language": "R",
"lines": 119,
"truncated": false,
"block": 10,
"row": 18358
},
{
"path": "2.Plots/Figure2/panel_c.R",
"sha256": "3191f78d3ce20eeada22a1b01d7aa66fc9a6a122dcc901612cb204c6d2f24324",
"language": "R",
"lines": 15,
"truncated": false,
"block": 10,
"row": 17889
},
{
"path": "2.Plots/Figure3/panel_b.R",
"sha256": "cc746f62ac33a60541bf4566c4343a3220319c33ed9d05acfb6c6ee165920ca3",
"language": "R",
"lines": 48,
"truncated": false,
"block": 10,
"row": 18170
},
{
"path": "2.Plots/Figure3/panel_c.R",
"sha256": "344b907772abd2bbc5f170bc6120ecfc4cc2b41178947c797d72e642d7bc594e",
"language": "R",
"lines": 25,
"truncated": false,
"block": 10,
"row": 17948
},
{
"path": "2.Plots/Figure3/panel_d.R",
"sha256": "fa1aeebe3999a09bab5dddc0628e56990ef08b3cf49baec84779655fd9e7a9b3",
"language": "R",
"lines": 25,
"truncated": false,
"block": 10,
"row": 17941
},
{
"path": "2.Plots/FigureE1/panel_c.R",
"sha256": "bd19eaba6001deed5c4edefd5a927ef0e811c83218a5651fb1028f76a193dc0c",
"language": "R",
"lines": 27,
"truncated": false,
"block": 10,
"row": 17928
},
{
"path": "2.Plots/FigureE1/panel_e.R",
"sha256": "cbd4482872e82665b69ff48f0989ef571b2c12f4f65ad019f9313a4466033eba",
"language": "R",
"lines": 19,
"truncated": false,
"block": 10,
"row": 17904
},
{
"path": "2.Plots/FigureE1/panel_g.R",
"sha256": "31393778ba7a8fb315e54a2ba2267bc0bdb9f75c28e86f3a7feb284c1b466107",
"language": "R",
"lines": 57,
"truncated": false,
"block": 10,
"row": 18255
},
{
"path": "2.Plots/FigureE2/4_GO_NMF_Fig_E2.R",
"sha256": "6214f4debbe86ab95fe4bc8fa272f75209402877956acaf2328103a62e09381d",
"language": "R",
"lines": 135,
"truncated": false,
"block": 10,
"row": 18420
},
{
"path": "2.Plots/FigureE2/6_Neuroepithelial_vs_embryonic_Fig_E2.Rmd",
"sha256": "0fac490067b1958c42cfca187986e14da7ef176357b0345fa96d5e0adb0f96ba",
"language": "R",
"lines": 326,
"truncated": false,
"block": 10,
"row": 18692
},
{
"path": "2.Plots/FigureE3/7_ZFTA_vs_Cluster3_Fig_E3.Rmd",
"sha256": "8aca77e649ce89922e47237749c72a5eeb31443173a6751938013a86b9b094e7",
"language": "R",
"lines": 505,
"truncated": false,
"block": 10,
"row": 18813
},
{
"path": "2.Plots/FigureE3/panel_a.R",
"sha256": "c9193315b78f15c42591d35ff69fa4e4ed61f43c000160ca4cc0e61aa939773a",
"language": "R",
"lines": 52,
"truncated": false,
"block": 10,
"row": 18211
},
{
"path": "2.Plots/FigureE4/panel_b.R",
"sha256": "d5273809ee380131e6636831a81e55e984575d46a3c7bdb6cf57eb4ea223d78b",
"language": "R",
"lines": 25,
"truncated": false,
"block": 10,
"row": 17934
},
{
"path": "2.Plots/FigureE4/panel_c.py",
"sha256": "22a9685d9b369692260483a16c125282204be0205b4dfd0b3e51e306c6017914",
"language": "Python",
"lines": 79,
"truncated": false,
"block": 10,
"row": 12631
},
{
"path": "2.Plots/FigureE4/panel_d.R",
"sha256": "ccb7f5f4bf7812a3af0a84fd3bd6eeea73c52ba66f838899a04e09ca42ae4fe5",
"language": "R",
"lines": 26,
"truncated": false,
"block": 10,
"row": 17946
},
{
"path": "2.Plots/FigureE4/panel_e.R",
"sha256": "7111977a7d4d5e852ce771856dcc97d458808080e4a2a0d29f05116b9b72c694",
"language": "R",
"lines": 27,
"truncated": false,
"block": 10,
"row": 17945
},
{
"path": "2.Plots/FigureE4/panel_f.R",
"sha256": "c98f244a051724a7331ce58bcfaece9bad775fe2a4b313fb932dc2eda8a47ad5",
"language": "R",
"lines": 25,
"truncated": false,
"block": 10,
"row": 17939
},
{
"path": "2.Plots/FigureE5/panel_a.R",
"sha256": "5e1712d08bebce4c10377855edf442d20a888562a59608956b27bfcc8674a23d",
"language": "R",
"lines": 37,
"truncated": false,
"block": 10,
"row": 17988
},
{
"path": "2.Plots/FigureE6/panel_a.R",
"sha256": "aca6495bec008bb59ff9852d1f6751a0b73cd847f1057039d2d2b0007962839b",
"language": "R",
"lines": 33,
"truncated": false,
"block": 10,
"row": 17967
},
{
"path": "2.Plots/FigureE6/panel_b.R",
"sha256": "e0564f369682fa51990692e3dfc785d1d0b4b5e6f72a075fadb1721030a5dc8a",
"language": "R",
"lines": 23,
"truncated": false,
"block": 10,
"row": 17930
},
{
"path": "2.Plots/FigureE8/panel_a.R",
"sha256": "9286608ca41e4a2303fa19662927d60367f33abe2eed8d8bc9c41c9f106088dd",
"language": "R",
"lines": 29,
"truncated": false,
"block": 10,
"row": 18050
},
{
"path": "2.Plots/Hierarchy.R",
"sha256": "0bb5f15eb32159c28e101c1a3540256d84c6b0748e20c31f653dce6c2126a786",
"language": "R",
"lines": 255,
"truncated": false,
"block": 10,
"row": 18726
},
{
"path": "3.Pseudobulk_analysis/1_dev_ref_preprocessing.R",
"sha256": "2430741736b27b287e33e70768eb86f70ec39cd7530922c6f1df1bfedf32ddac",
"language": "R",
"lines": 188,
"truncated": false,
"block": 10,
"row": 18534
},
{
"path": "3.Pseudobulk_analysis/2_dev_ref_dataset_processing2.R",
"sha256": "5aa114c8b53b33643fe5dd926d8df1f242017b53847816e96ee6b3ea3ef72cf6",
"language": "R",
"lines": 196,
"truncated": false,
"block": 10,
"row": 18585
},
{
"path": "3.Pseudobulk_analysis/3_projection_tumor_to_ref.R",
"sha256": "606be519d8013c8e3263c803cfbb66efd300886252331ad35a4e0a6f39dcfa90",
"language": "R",
"lines": 267,
"truncated": false,
"block": 10,
"row": 18705
},
{
"path": "3.Pseudobulk_analysis/Scoring_validation_dataset_FigE3e.R",
"sha256": "8313126f27e6989e325b85bf023ac5d520595c0b08889aed80e1a518d8f6cb94",
"language": "R",
"lines": 203,
"truncated": false,
"block": 10,
"row": 18573
},
{
"path": "3.Pseudobulk_analysis/resources/NMF_helper_function.R",
"sha256": "db417371968fff7d4d47bc106bf71e942e12557f1c1b604eb5cc78ab7752f834",
"language": "R",
"lines": 239,
"truncated": false,
"block": 10,
"row": 18576
},
{
"path": "3.Pseudobulk_analysis/resources/Plot_style_v2.R",
"sha256": "9db72c7c3349b6935ffa44b3fcffb48b7fb4bc64198889fdc3a4a6e89de2595a",
"language": "R",
"lines": 155,
"truncated": false,
"block": 10,
"row": 18547
},
{
"path": "3.Pseudobulk_analysis/resources/single_cell_preprocessing_helper_functions_SD_240131.R",
"sha256": "af64b20d344fd1465036ed80bda4d9cd6545c040ad772b687429c5208adddf47",
"language": "R",
"lines": 1166,
"truncated": false,
"block": 10,
"row": 18944
},
{
"path": "4.Xenium/.ipynb_checkpoints/3_Sara_neighborhood_20231020-checkpoint.ipynb",
"sha256": "32dfe0ac60476d59289ccc156a75ec09708cf2cc4b5eba2f9c31195f504999ed",
"language": "Jupyter",
"lines": 221,
"truncated": false,
"block": 10,
"row": 5536
},
{
"path": "4.Xenium/.ipynb_checkpoints/Neighbors-Daeun.nbconvert-checkpoint.ipynb",
"sha256": "8ca25967bd52ef895fabef6297952a640fcfd650589c6e45493016dfc32a6de1",
"language": "Jupyter",
"lines": 475,
"truncated": false,
"block": 10,
"row": 5769
},
{
"path": "4.Xenium/0_preparation_scRNAseq_data.R",
"sha256": "44821c1490180c25512e4d71e4b96f7d27dd34219a99077f0fd8926f5f23cfea",
"language": "R",
"lines": 27,
"truncated": false,
"block": 10,
"row": 17990
},
{
"path": "4.Xenium/1_preprocessing.R",
"sha256": "6b5edae81409120cfc6a483fc13891bb85da6d456eafcd352db69b77043d13d7",
"language": "R",
"lines": 35,
"truncated": false,
"block": 10,
"row": 18013
},
{
"path": "4.Xenium/2_assign_programs.R",
"sha256": "70e048cb1b3773befca52d0d1e224eb7e1b4e73b148f9f160a61cb743cca97b6",
"language": "R",
"lines": 47,
"truncated": false,
"block": 10,
"row": 18065
},
{
"path": "4.Xenium/3_NicheAnalysis.R",
"sha256": "0f958c6dbd6a932a10d5f2ce4155109405434c6b72f9f61b920c37745f68b3b5",
"language": "R",
"lines": 39,
"truncated": false,
"block": 10,
"row": 18029
},
{
"path": "4.Xenium/4_coherence.R",
"sha256": "861a1b3dd98490978b82db8a4e9283b1d6387191d5cf5084bcc3bc6f3c28dae7",
"language": "R",
"lines": 60,
"truncated": false,
"block": 10,
"row": 18276
},
{
"path": "4.Xenium/cellcharter/ST_EPN_cellcharter_k26.ipynb",
"sha256": "2630576356140f6206c41ac9ca241b7e26022effc820bb87a8f85fd89fb96e15",
"language": "Jupyter",
"lines": 62,
"truncated": false,
"block": 10,
"row": 4918
},
{
"path": "4.Xenium/cellcharter/ST_EPN_scanpy.ipynb",
"sha256": "82bd7b5bdcbdd71407634f9f34de7cb75e961b6f5ef58686da88fb960c9e2cf7",
"language": "Jupyter",
"lines": 50,
"truncated": false,
"block": 10,
"row": 4904
},
{
"path": "4.Xenium/cellcharter/ST_EPN_scvi.ipynb",
"sha256": "e58280e749ae92a1f55aaaac627548eccc54b9a1c7c4c3bbaa30122a5571b616",
"language": "Jupyter",
"lines": 63,
"truncated": false,
"block": 10,
"row": 4925
},
{
"path": "4.Xenium/cellcharter/Sample_Spatial_Cluster_Heatmap.Rmd",
"sha256": "77fe126bf976c7be52e07cc8d2757f49f7751f755f114d236e0e2abb08ec5d4d",
"language": "R",
"lines": 288,
"truncated": false,
"block": 10,
"row": 18597
},
{
"path": "4.Xenium/cellcharter/SpatialCluster_MetaNiche_Correlation.Rmd",
"sha256": "ca99bd98a20e8cd3497ad9202f4425e6a904c9f5ba86ca873eaa8de53d689927",
"language": "R",
"lines": 231,
"truncated": false,
"block": 10,
"row": 18575
},
{
"path": "4.Xenium/cellcharter/SpatialCluster_Metaprogram_Composition.Rmd",
"sha256": "16626610b8e781096d1ddc52ac7c17c788194c251370cd16a5e66aa09513136e",
"language": "R",
"lines": 100,
"truncated": false,
"block": 10,
"row": 18244
},
{
"path": "4.Xenium/cellcharter/Tumor_TME_Entropy_Comparison.Rmd",
"sha256": "c227dea9e10e41f3573e320d7515483d90596fac7dc1fd301cd2fedbac3411de",
"language": "R",
"lines": 120,
"truncated": false,
"block": 10,
"row": 18294
},
{
"path": "4.Xenium/resources/FLXenium/annot.R",
"sha256": "3d66882e133bf95f0864d9e0a8dece4238b7328e6336490659318704c24fec62",
"language": "R",
"lines": 490,
"truncated": false,
"block": 10,
"row": 18894
},
{
"path": "4.Xenium/resources/FLXenium/main.R",
"sha256": "5270c564504a91b804b0a322b947a826e8678a1f24007af153940ddc210200d9",
"language": "R",
"lines": 45,
"truncated": false,
"block": 10,
"row": 18025
},
{
"path": "4.Xenium/resources/FLXenium/niche.R",
"sha256": "edf85764f4240dbcb949388684798aa53ae4944fed8463c45aaacc43b235095d",
"language": "R",
"lines": 249,
"truncated": false,
"block": 10,
"row": 18787
},
{
"path": "4.Xenium/resources/FLXenium/prep.R",
"sha256": "968d868c16b05edd024fcc733383eeb99920e9894ba87d0b0d52c67112cc4dcd",
"language": "R",
"lines": 75,
"truncated": false,
"block": 10,
"row": 18375
},
{
"path": "4.Xenium/resources/FLXenium/spat.R",
"sha256": "6ca5ee135f0fa45e07dbb0359c5236b798e1c53713ed879f63d005576ca47b8e",
"language": "R",
"lines": 258,
"truncated": false,
"block": 10,
"row": 18738
},
{
"path": "4.Xenium/resources/FLXenium/utils.R",
"sha256": "5f8ca0ba65a662b28f61d6d707883e8e1f279f8c56ecb20fdffb510131e54e03",
"language": "R",
"lines": 1745,
"truncated": false,
"block": 10,
"row": 18968
},
{
"path": "4.Xenium/resources/color_palette.R",
"sha256": "7f2dba87743dc230bda4c3b2a8be762e7c38cfdc9d683a2b8d289b09de275633",
"language": "R",
"lines": 245,
"truncated": false,
"block": 10,
"row": 18683
},
{
"path": "4.Xenium/resources/epn_functions.R",
"sha256": "f54fae0f9e2c273b680f2355b98205e2b309e3dcc3a3d711e892f266ecf763f3",
"language": "R",
"lines": 1377,
"truncated": false,
"block": 10,
"row": 18965
},
{
"path": "5.Co-culture/0_Preprocessing.R",
"sha256": "c032f2c76d3ba37466cb9c5c3ef9eb93b1ab98b69edbf5828a7875e34e5df0e0",
"language": "R",
"lines": 337,
"truncated": false,
"block": 10,
"row": 18797
},
{
"path": "5.Co-culture/0_tdTomato_Reference.sh",
"sha256": "7f12624ec3e4b2d5aefac0978be07b1c3f2d87eaa4f35148101c4a66cb56a3f1",
"language": "Shell",
"lines": 220,
"truncated": false,
"block": 10,
"row": 19647
},
{
"path": "5.Co-culture/1_InferCNV.R",
"sha256": "f5af304687c4f9efe6250372ac5c79a084ded492f737219f90714e536eb49bb5",
"language": "R",
"lines": 531,
"truncated": false,
"block": 10,
"row": 18882
},
{
"path": "5.Co-culture/2_Processing_coculture.Rmd",
"sha256": "f354226731485ff7292fa2a7b27a78d8a3f0e2b2fe7ace10de2adc2d1177d4dd",
"language": "R",
"lines": 479,
"truncated": false,
"block": 10,
"row": 18806
},
{
"path": "5.Co-culture/3_heatmap.Rmd",
"sha256": "20ddc655c7ec2b8690a05c393961d61d57df9ad13f57cdd7e379f3f33d23a1b1",
"language": "R",
"lines": 166,
"truncated": false,
"block": 10,
"row": 18442
},
{
"path": "5.Co-culture/4_Coculture_rat_celltypes.Rmd",
"sha256": "3f2de775ef21c2a43bf403d51e7ae9c155f018cbac308bf4e54932199fd7c84a",
"language": "R",
"lines": 539,
"truncated": false,
"block": 10,
"row": 18839
},
{
"path": "5.Co-culture/5_DEG_pathways.Rmd",
"sha256": "4a0695392b6bbe480e2b72f178f3aaf6bbd7436712d547fd0e22612f7bb13fac",
"language": "R",
"lines": 491,
"truncated": false,
"block": 10,
"row": 18857
},
{
"path": "5.Co-culture/6_PseudoDEG.Rmd",
"sha256": "a85e0ee727ce15bd546913c5bc223361d250e7ac7cc054654a81eedd446a8501",
"language": "R",
"lines": 592,
"truncated": false,
"block": 10,
"row": 18878
},
{
"path": "5.Co-culture/7_EP1NS_hiNs.Rmd",
"sha256": "1697ec473c2b61588b8cf73043e967fd8acc39180ad7628c403d4b4361b56257",
"language": "R",
"lines": 624,
"truncated": false,
"block": 10,
"row": 18848
},
{
"path": "5.Co-culture/resources/NMF_helper_function.R",
"sha256": "db417371968fff7d4d47bc106bf71e942e12557f1c1b604eb5cc78ab7752f834",
"language": "R",
"lines": 239,
"truncated": false,
"block": 10,
"row": 18576
},
{
"path": "5.Co-culture/resources/Plot_style_v2.R",
"sha256": "de9e45c68c68d5ee32df6055f4973b8562df8fb75a30f295efdfbad70e4a5286",
"language": "R",
"lines": 74,
"truncated": false,
"block": 10,
"row": 18330
},
{
"path": "5.Co-culture/resources/single_cell_preprocessing_helper_functions.R",
"sha256": "219d20f3e472eb11fa4efb736e300bfc6002d3a93fcf25d18b99effe91443ac0",
"language": "R",
"lines": 1158,
"truncated": false,
"block": 10,
"row": 18940
},
{
"path": "6.Preclinical_models/1-filtering.R",
"sha256": "881e2e4d828a5bf2efbaae762f45000b14166a30878c57f4fc96e93f6d3f8743",
"language": "R",
"lines": 275,
"truncated": false,
"block": 10,
"row": 18763
},
{
"path": "6.Preclinical_models/2-Plots.R",
"sha256": "7c79805cafc72ba7b19128c3ab732dceef09ed7c8832a33826eb4206f37adf52",
"language": "R",
"lines": 68,
"truncated": false,
"block": 10,
"row": 18273
},
{
"path": "6.Preclinical_models/3-Downstream.R",
"sha256": "3c03e6f29e2a0cebce3132c1508e6213ebdf651b5519957dccb0945e781b0b96",
"language": "R",
"lines": 199,
"truncated": false,
"block": 10,
"row": 18580
},
{
"path": "6.Preclinical_models/resources/NMF_helper_function.R",
"sha256": "db417371968fff7d4d47bc106bf71e942e12557f1c1b604eb5cc78ab7752f834",
"language": "R",
"lines": 239,
"truncated": false,
"block": 10,
"row": 18576
},
{
"path": "6.Preclinical_models/resources/Plot_style.R",
"sha256": "111709729a665ac5bbe2b1ef6745b99369a84917f21dc012e220b0270659550d",
"language": "R",
"lines": 68,
"truncated": false,
"block": 10,
"row": 18286
},
{
"path": "6.Preclinical_models/resources/Plotting_helper_functions.R",
"sha256": "bde86f753225f4b41ba8dc3720a3574c6d80922eed7d9c103044d5fd8c41916f",
"language": "R",
"lines": 520,
"truncated": false,
"block": 10,
"row": 18859
},
{
"path": "6.Preclinical_models/resources/functions.R",
"sha256": "ce065ae3f33997f6a0c50adc00b45e4a739887a385bbf1f4ba1d3ad6d2cc7f14",
"language": "R",
"lines": 12,
"truncated": false,
"block": 10,
"row": 17878
},
{
"path": "6.Preclinical_models/resources/plotutils.R",
"sha256": "12bec5da7492020e645bb3df17972ad0081092986dd227473c98a0430ba904d5",
"language": "R",
"lines": 238,
"truncated": false,
"block": 10,
"row": 18704
},
{
"path": "6.Preclinical_models/resources/single_cell_preprocessing_helper_functions.R",
"sha256": "219d20f3e472eb11fa4efb736e300bfc6002d3a93fcf25d18b99effe91443ac0",
"language": "R",
"lines": 1158,
"truncated": false,
"block": 10,
"row": 18940
},
{
"path": "LICENSE",
"sha256": "86595c18733b194a58e8f6d8edfb34d8dd7d856680a2395f4841e5be6c6697e9",
"language": "License",
"lines": 21,
"truncated": false,
"block": 10,
"row": 6118
},
{
"path": "README.md",
"sha256": "668411c49b4ef75697e0b73681cc24f15f22f3a341b8f4af5f43612dec00e58f",
"language": "Text",
"lines": 55,
"truncated": false,
"block": 10,
"row": 19874
},
{
"path": "resources/Functions.R",
"sha256": "ed410be79647aa2a3902218ec7a547bbd038ca9ee2c9d3ee763f8c6f3a67bb55",
"language": "R",
"lines": 8,
"truncated": false,
"block": 10,
"row": 17863
},
{
"path": "resources/NMF_helper_function.R",
"sha256": "db417371968fff7d4d47bc106bf71e942e12557f1c1b604eb5cc78ab7752f834",
"language": "R",
"lines": 239,
"truncated": false,
"block": 10,
"row": 18576
},
{
"path": "resources/Plot_style.R",
"sha256": "4758f4a8b1b60035400efe6080300b65b36c4bb3eb55123e0d6b092b296fdd58",
"language": "R",
"lines": 53,
"truncated": false,
"block": 10,
"row": 18202
},
{
"path": "resources/single_cell_preprocessing_helper_functions_CBJr.R",
"sha256": "8f1e4567e84a855209e536de018a0427efeac4e2c238267b6d93dc16ef0d8016",
"language": "R",
"lines": 1280,
"truncated": false,
"block": 10,
"row": 18953
},
{
"path": "resources/single_cell_preprocessing_helper_functions_SD_240131.R",
"sha256": "30ee255f12440008e9b8e751df74fef0bc9590efd9c49bcb58afbb67572749bb",
"language": "R",
"lines": 1269,
"truncated": false,
"block": 10,
"row": 18952
}
]
}