{ "format": "oscr-script-manifest/1", "repository": "zenodo:17180220", "url": "https://doi.org/10.5281/zenodo.17180220", "host": "zenodo.org", "commit": "", "license": "CC-BY-4.0", "license_confirmed_by": "license of the archive's record", "redistribution": "yes", "files": [ { "path": "01-hvg-mapping_neuron_analysis.py", "sha256": "f153da5a176082d30cf9c53038e2bc4f5e733fd9f87330a6871a4c7be10eabaf", "language": "Python", "lines": 63, "truncated": false, "block": 15, "row": 10450 }, { "path": "01_csv-export_revisions.R", "sha256": "9d9fb7bc5db12d8d4843f8e2973b345f81eb68a081bb2b77e7ffc06202d1530a", "language": "R", "lines": 46, "truncated": false, "block": 16, "row": 2232 }, { "path": "01_pp_global_analysis.py", "sha256": "89862e62bd8ae9a2ffc14c31fbccb3cd9c749139715d3642e837e158203c7caf", "language": "Python", "lines": 306, "truncated": false, "block": 15, "row": 23032 }, { "path": "02-pairwise-de-wald-cell_type-normalized_neuron_analysis.py", "sha256": "29cce7ce44847723e6ea4ebe5f33bb5fe53ca209ca3a55595ffccdd7c35d6781", "language": "Python", "lines": 263, "truncated": false, "block": 15, "row": 21037 }, { "path": "02_create-anndata_revisions.ipynb", "sha256": "38c3dc41f19816f0c74e75d859a12aec66b74d6cd07b82d2a7a6592c5880067e", "language": "Jupyter", "lines": 39, "truncated": false, "block": 14, "row": 14816 }, { "path": "02_integration-rivanna_global_analysis.ipynb", "sha256": "acb8773e8a45a28021d741e2b4aaf6a17f92dbbce3ee734125a039c9a3547f13", "language": "Jupyter", "lines": 270, "truncated": false, "block": 14, "row": 15367 }, { "path": "03-pairwise-de-wald-cell_type-normalized-volcano_neuron_analysis.R", "sha256": "37b7834461d9bdf9af4178764c0fd86e605268227d997ca64856770a6124c788", "language": "R", "lines": 93, "truncated": false, "block": 16, "row": 2663 }, { "path": "03_eda-1_global_analysis.py", "sha256": "f8cf0ade76b01a7fb75044454e0b7d1ffba8629d360eaf2f426fb359b7f3f33d", "language": "Python", "lines": 238, "truncated": false, "block": 15, "row": 20491 }, { "path": "04-pairwise-select-volcano_neuron_analysis.R", "sha256": "b69a2ea93a42a4f59ffd8b204ece041620d0c6fc767e50089d787d8f7b2586e5", "language": "R", "lines": 181, "truncated": false, "block": 16, "row": 3309 }, { "path": "04_create-anndata_revisions.ipynb", "sha256": "59400206b8de7d457d7b0ef574a4100b3e68289243d596520ea2f9e87eeb7ed5", "language": "Jupyter", "lines": 58, "truncated": false, "block": 14, "row": 14935 }, { "path": "04_eda-2_global_analysis.py", "sha256": "62e9f6e5d5795b5e69f5fcecd3ba44edd1ee354e553c9bf497c32e23c6904f65", "language": "Python", "lines": 145, "truncated": false, "block": 15, "row": 16570 }, { "path": "05-neurons-rivanna-integration_neuron_analysis.py", "sha256": "78c41d2ebae8c3de5f39ab90f680e36c956d6e86d42e8d578cafdb2ca26f6172", "language": "Python", "lines": 129, "truncated": false, "block": 15, "row": 13375 }, { "path": "05_annotation_global_analysis.py", "sha256": "97ad75ee979644b000569c7315c774bdd330fb28352e123205767b761f545950", "language": "Python", "lines": 288, "truncated": false, "block": 15, "row": 20753 }, { "path": "05_mg-analysis_revisions.ipynb", "sha256": "66d18ae5201408bcdd0683812cd77e16afb338e5c2a043b8cd9d56dc4a797869", "language": "Jupyter", "lines": 255, "truncated": false, "block": 14, "row": 16161 }, { "path": "05b_cd45-pp_revisions.ipynb", "sha256": "04a842589058e861e2e18c3c1cf6577475139e5b0d86fadaa64d127f587150e1", "language": "Jupyter", "lines": 113, "truncated": false, "block": 14, "row": 14960 }, { "path": "06-create-neuron-subset-files_neuron_analysis.py", "sha256": "e86edbb35a6fe9bad971a978019896d200c57bcb71bcd80602feb3008d92694a", "language": "Python", "lines": 168, "truncated": false, "block": 15, "row": 16202 }, { "path": "06_de-wald-cell_type_global_analysis.py", "sha256": "6c5401677b627cda49316e29fed0df8c7bdfa7b055a5a9c5841f93c7a7ca5aaf", "language": "Python", "lines": 377, "truncated": false, "block": 15, "row": 24142 }, { "path": "06_neurons-soupx_revisions.ipynb", "sha256": "ef82351538d53249c1dadcd51d99d9ec762290a6a8015ca0d508516f453951c5", "language": "Jupyter", "lines": 141, "truncated": false, "block": 14, "row": 15217 }, { "path": "07-neuron-clusters-general-viz_neuron_analysis.py", "sha256": "343f73ddd9b81850a475a22ccd8a484ccbdc0fa6cf9f359d27b810cfa9a4e5e5", "language": "Python", "lines": 219, "truncated": false, "block": 15, "row": 19179 }, { "path": "07_de-wald-cluster_global_analysis.py", "sha256": "cc30a5864e345c07878a6b883cd70feda3931403a9431e70409385192cbc3e3d", "language": "Python", "lines": 368, "truncated": false, "block": 15, "row": 23929 }, { "path": "07_neurons-scvi_revisions.ipynb", "sha256": "db684e633fde41aa5a6bb4d204203c63f46a858fd33e4654fc8785d8b6de88fa", "language": "Jupyter", "lines": 123, "truncated": false, "block": 14, "row": 14963 }, { "path": "08-neuron-clusters-of-interest_neuron_analysis.py", "sha256": "3c74ddc6d9acda6a3fcf0a7425eddeab280394bf5d25da01711ecc5c7e4d50e5", "language": "Python", "lines": 186, "truncated": false, "block": 15, "row": 18770 }, { "path": "08_de-scvi-cell_type_global_analysis.py", "sha256": "92f84e1340d0a54b32c23e655644c27eed2e276364373470b18d0a9d7d8437b0", "language": "Python", "lines": 168, "truncated": false, "block": 15, "row": 17902 }, { "path": "08_neuronal-analysis_revisions.ipynb", "sha256": "5cd630db5e154644766f63b5909d8668191bd5330b6831bbca53641937599129", "language": "Jupyter", "lines": 1246, "truncated": false, "block": 14, "row": 16587 }, { "path": "09_de-log2fc-check_global_analysis.py", "sha256": "090618b2235c69dc9dd1fa62e5f9d7baf85db13f727b9f8819d49ca806710cf4", "language": "Python", "lines": 208, "truncated": false, "block": 15, "row": 21689 }, { "path": "09_pathway-enrichment_revisions.ipynb", "sha256": "bfb915c98ab01fdaea56f400410cc13e34737e8ba35d5cf784295ecb9055f91a", "language": "Jupyter", "lines": 272, "truncated": false, "block": 14, "row": 15713 }, { "path": "09_update-annotations_neuron_analysis.py", "sha256": "6733206d12aef9634abc653d2a3757a429b8097764f8e82b2ad57bcad3a5b182", "language": "Python", "lines": 57, "truncated": false, "block": 15, "row": 9903 }, { "path": "10_input-vs-hippo_revisions.ipynb", "sha256": "7b5df2f7ddb3aa6bea72ab9b01e7fe1395c7b86c8710edcccc9838743e2cf785", "language": "Jupyter", "lines": 423, "truncated": false, "block": 14, "row": 16042 }, { "path": "10_update-wald-test-cell_type_neuron_analysis.py", "sha256": "d4803ebbf2aaa9c57d3e64b3c19ba2b6713b1b18f7d4a2b6760265610e3d6ff7", "language": "Python", "lines": 240, "truncated": false, "block": 15, "row": 20793 }, { "path": "10_volcano-plots_global_analysis.R", "sha256": "9a9cace8d086d0978a2e0fb6d6c7545fa4635f36ec118a9ab0c09ccef58214ed", "language": "R", "lines": 89, "truncated": false, "block": 16, "row": 2642 }, { "path": "11_data-visualization_global_analysis.py", "sha256": "11bbab477fee8b54670122d678996fc70e291c9612676b1fdedc4ac4960ed966", "language": "Python", "lines": 311, "truncated": false, "block": 15, "row": 22678 }, { "path": "11_figures_neuron_analysis.py", "sha256": "343f47d4f705aa9a590f82c5be06811240416ae1ae5b0f6b0dccb2c42b43b049", "language": "Python", "lines": 414, "truncated": false, "block": 15, "row": 24322 }, { "path": "12_Figure_04-volcano-plots_neuron_analysis.R", "sha256": "fec136da2bdc8388a71379e8611297eb3711f3f10b17424f0a09b03949ed963f", "language": "R", "lines": 194, "truncated": false, "block": 16, "row": 3290 }, { "path": "12_data-viz-degs_global_analysis.py", "sha256": "6bc2c6a7c385c2a4e70bb145bc88ebaa868f0c13dadc65ad0db0b94083ec5ef1", "language": "Python", "lines": 389, "truncated": false, "block": 15, "row": 23746 }, { "path": "13_go-kegg-enrichment_global_analysis.py", "sha256": "d46711cc3908db5e444093741ae78ef895735e25baa1b1f2f4b48307d8ee2e8a", "language": "Python", "lines": 120, "truncated": false, "block": 15, "row": 15999 }, { "path": "14_export-hvg-dataset_global_analysis.py", "sha256": "790da61271036922cf6a705d04c66d27fe6153ec802c13eae85647d45c84155d", "language": "Python", "lines": 121, "truncated": false, "block": 15, "row": 16205 }, { "path": "15_export-full-dataset_global_analysis.py", "sha256": "94a6ef3f69c07ecb3d23fc0238679bcaa3c64f35621aaea1fcab2caf4c054b88", "language": "Python", "lines": 117, "truncated": false, "block": 15, "row": 16047 }, { "path": "16_seurat-conversion_global_analysis.R", "sha256": "6136fd001553f2336ab22ba65a2a60e6ae14e6ac0febc277213c047d4e5457b0", "language": "R", "lines": 191, "truncated": false, "block": 16, "row": 3514 }, { "path": "hvg-full-mapping_global_analysis.py", "sha256": "8b229afb30ceae9ea3151de703a60b23fb12e0f71c9b6722e409d3489365f335", "language": "Python", "lines": 62, "truncated": false, "block": 15, "row": 10448 }, { "path": "run_soupx_revisions.R", "sha256": "17d9ee3c7dd2fb385000e0990b1bf4b5392b7aea44010c4dfd54a89735b07cde", "language": "R", "lines": 90, "truncated": false, "block": 16, "row": 2601 }, { "path": "solo_revisions.py", "sha256": "0f76d3d94a0208d4ed16f2c64e21ae8b2fee945d67790a02712a44f7e2aa1219", "language": "Python", "lines": 44, "truncated": false, "block": 15, "row": 9399 } ] }