{ "format": "oscr-script-manifest/1", "repository": "zenodo:19640367", "url": "10.5281/zenodo.19640367", "host": "zenodo.org", "commit": "", "license": "CC-BY-4.0", "license_confirmed_by": "license of the archive's record", "redistribution": "yes", "files": [ { "path": "00.Geneset.R", "sha256": "94a04bc2fa5ce41b68b05773260cffa1f5c3fed62ff151d8d9c63792b85d855e", "language": "R", "lines": 184, "truncated": false, "block": 8, "row": 3888 }, { "path": "README.md", "sha256": "835beb4a252a2805bd234c904ea08677484bbb8a8794fe37b37e715550a5269f", "language": "Text", "lines": 2, "truncated": false, "block": 8, "row": 9479 }, { "path": "README.txt", "sha256": "63486df4d0688d91256794f9e79dc79071f3326632fd07d58a8da9c607de36da", "language": "Text", "lines": 541, "truncated": false, "block": 8, "row": 10831 }, { "path": "RNA_Animal/00.Matrix_MR.R", "sha256": "05a1166dcc9d44f439fda07b7db9c577f5ff74f02948a069666ff17a018c0fd5", "language": "R", "lines": 57, "truncated": false, "block": 8, "row": 2821 }, { "path": "RNA_Animal/00.Subgrouping_MR.R", "sha256": "79e26f64f813830a0b19d05f218e7684e32847321126c5849a4cf09c34558e35", "language": "R", "lines": 99, "truncated": false, "block": 8, "row": 3579 }, { "path": "RNA_Animal/01.Pre-processing/03.fastp_paired.sh", "sha256": "b37916a51438265802aac116396031fe158daf82052e243d0969a0607a1cc843", "language": "Shell", "lines": 27, "truncated": false, "block": 8, "row": 7039 }, { "path": "RNA_Animal/01.Pre-processing/03.fastp_single.sh", "sha256": "875920655558c4a21e2a3b067ea96ca15b0da820cc59a5d0629061ed894b7fac", "language": "Shell", "lines": 24, "truncated": false, "block": 8, "row": 6899 }, { "path": "RNA_Animal/01.Pre-processing/04.Indexing_Mouse.sh", "sha256": "37ee05d62576ffdbd87d97375f16fd04a312d88ce7410cb87718e25e81f7e643", "language": "Shell", "lines": 81, "truncated": false, "block": 8, "row": 8297 }, { "path": "RNA_Animal/01.Pre-processing/04.Indexing_Rat.sh", "sha256": "2557a1cd8e268709498bc305d78302d5b33aa7796e656792469ad7aaafe2fbc5", "language": "Shell", "lines": 81, "truncated": false, "block": 8, "row": 8314 }, { "path": "RNA_Animal/01.Pre-processing/04.aligned_M_Paired_100.sh", "sha256": "b8d4e97a5e9a2942bb0c83c39a90c4b8754f1ca98c1956c36cd092db3813e2b3", "language": "Shell", "lines": 46, "truncated": false, "block": 8, "row": 7808 }, { "path": "RNA_Animal/01.Pre-processing/04.aligned_M_Paired_125.sh", "sha256": "b0d939299f1ca749fb9a901654f4a69555ee6342e2ef2f431bfd2c624745ba07", "language": "Shell", "lines": 46, "truncated": false, "block": 8, "row": 7807 }, { "path": "RNA_Animal/01.Pre-processing/04.aligned_M_Paired_150.sh", "sha256": "d8e58a6a41ab5eae0763491af40d4091aaf7f2de3c5b1d4699e723af5e8b6df3", "language": "Shell", "lines": 46, "truncated": false, "block": 8, "row": 7809 }, { "path": "RNA_Animal/01.Pre-processing/04.aligned_M_Paired_35.sh", "sha256": "004269edcf488118f4ce6448dbf66ea5db15d3a7026dc208167edbba0dbd7e8a", "language": "Shell", "lines": 46, "truncated": false, "block": 8, "row": 7802 }, { "path": "RNA_Animal/01.Pre-processing/04.aligned_M_Paired_50.sh", "sha256": "393b5189abe4f2445f84cf610381e166737b61e3bef17c196eb1edf036f58a6a", "language": "Shell", "lines": 46, "truncated": false, "block": 8, "row": 7803 }, { "path": "RNA_Animal/01.Pre-processing/04.aligned_M_Single_50.sh", "sha256": "06e738f41145ed879b10a2cff31134ef73bbd40dcf83683e24a32a65a04b0a46", "language": "Shell", "lines": 45, "truncated": false, "block": 8, "row": 7712 }, { "path": "RNA_Animal/01.Pre-processing/04.aligned_M_Single_75.sh", "sha256": "8adcfe96f5aa7669c843843176581d7ce825e29123d8a49495a3e4099b84dcbe", "language": "Shell", "lines": 45, "truncated": false, "block": 8, "row": 7713 }, { "path": "RNA_Animal/01.Pre-processing/04.aligned_R_Paired_125.sh", "sha256": "ce7d5167c10737f2eb864cf01ea6d440211514fbb8d6db413f49f7f5f1815580", "language": "Shell", "lines": 46, "truncated": false, "block": 8, "row": 7811 }, { "path": "RNA_Animal/01.Pre-processing/04.aligned_R_Paired_150.sh", "sha256": "07426778974d5f099649f4e19bd9819c0ff184ceaf7234eef11bd8b1c8174299", "language": "Shell", "lines": 46, "truncated": false, "block": 8, "row": 7810 }, { "path": "RNA_Animal/01.Pre-processing/04.aligned_R_Paired_75.sh", "sha256": "9c78cadee9fcb4ad4aa311acc87903014f098b7834c1bfe9afcba22a4011017c", "language": "Shell", "lines": 46, "truncated": false, "block": 8, "row": 7805 }, { "path": "RNA_Animal/01.Pre-processing/04.aligned_R_Single_35.sh", "sha256": "1b9ecf08425417c596ade0e73ba38043a6709f2bbac661fdf13b07fd63737b41", "language": "Shell", "lines": 45, "truncated": false, "block": 8, "row": 7714 }, { "path": "RNA_Animal/02.Quantification/01.HTseq_M.sh", "sha256": "b7afce00e8544e2f4f24b02d8238a476fb0ce5bfd3d55bd64ab409773ccd7fa1", "language": "Shell", "lines": 28, "truncated": false, "block": 8, "row": 6857 }, { "path": "RNA_Animal/02.Quantification/01.HTseq_R.sh", "sha256": "29e1376f1ef94f1c4dc8bdcccdc81c2c36c12d1c6e2c1099cd7efcee558dc077", "language": "Shell", "lines": 28, "truncated": false, "block": 8, "row": 6859 }, { "path": "RNA_Animal/02.Quantification/02.gtf_table.R", "sha256": "e2e7646fe32645f74e3e364d1990e8686ac1ac9e5b89f7fe8274f3dd55208c92", "language": "R", "lines": 42, "truncated": false, "block": 8, "row": 1986 }, { "path": "RNA_Animal/02.Quantification/03.Matrix.R", "sha256": "73972858c28d61c31ff4b4454d3368ae06ef7d2ed9f3a7bd6b3bc100f64edb78", "language": "R", "lines": 107, "truncated": false, "block": 8, "row": 3400 }, { "path": "RNA_Animal/02.Quantification/04.combat.R", "sha256": "f26d04ea20c7cafdcbbf1807341aa172385fdb3a5fa1af8903f5d9f6f54335cf", "language": "R", "lines": 29, "truncated": false, "block": 8, "row": 1600 }, { "path": "RNA_Animal/03.Normalization/01.TPM_normalization.R", "sha256": "9c818aa1d24c4d329d728c7bcdb9cf9d786611e06ec865dfb951cf1e1ce67dda", "language": "R", "lines": 127, "truncated": false, "block": 8, "row": 3457 }, { "path": "RNA_Animal/04.Clustering/01.Count_PCA_M.R", "sha256": "c8b301bdc18dee6f278220be3f7a248428b20af7185e714573faf69ad3e58248", "language": "R", "lines": 145, "truncated": false, "block": 8, "row": 3511 }, { "path": "RNA_Animal/04.Clustering/01.Count_PCA_R.R", "sha256": "d4bf48ec1bf39f71064211e7b1c57e984187bb045314c352d3435aba8c81abd7", "language": "R", "lines": 143, "truncated": false, "block": 8, "row": 3485 }, { "path": "RNA_Animal/04.Clustering/01.TPM_PCA_M.R", "sha256": "5bb03a61c053990c9b8eaa13c6fcb82b4b1a596addf9d0f7a6c2709372262385", "language": "R", "lines": 120, "truncated": false, "block": 8, "row": 3105 }, { "path": "RNA_Animal/04.Clustering/01.TPM_PCA_R.R", "sha256": "0e122c1921b675f8df695279301e2981f733a7a6d5410dbb53ea98b452807f30", "language": "R", "lines": 118, "truncated": false, "block": 8, "row": 3077 }, { "path": "RNA_Animal/05.DESeq/02.DESeq_M_ALL.R", "sha256": "f7db6b9bc72a464353b408a788ea99c8b9c52dc58b533cb0b1f86859418bee78", "language": "R", "lines": 27, "truncated": false, "block": 8, "row": 1655 }, { "path": "RNA_Animal/05.DESeq/02.DESeq_M_KAI_IA.R", "sha256": "ea4c70046ec78d0cfbc2f7ff00fdfa25543fe218d3b7ad04605f87c940dd7f95", "language": "R", "lines": 68, "truncated": false, "block": 8, "row": 2454 }, { "path": "RNA_Animal/05.DESeq/02.DESeq_M_KAI_IH.R", "sha256": "4ec856e6df510021fc1c49c4bfa7ece05b53e65c15a323218ced5239e059a851", "language": "R", "lines": 97, "truncated": false, "block": 8, "row": 3102 }, { "path": "RNA_Animal/05.DESeq/02.DESeq_M_KAI_IP.R", "sha256": "9f45a68f5133f57cfea14a9a7fdfe5496963cb29b01b473e6d74ecdfebd254e6", "language": "R", "lines": 52, "truncated": false, "block": 8, "row": 2058 }, { "path": "RNA_Animal/05.DESeq/02.DESeq_M_PILO.R", "sha256": "103a8ae138c6ac9ec86f21830908b9c045f22d991279ab86f694c938a9c1da70", "language": "R", "lines": 74, "truncated": false, "block": 8, "row": 2587 }, { "path": "RNA_Animal/05.DESeq/02.DESeq_R_ALL.R", "sha256": "db274e689f31c9728e8fbe0ac53f2073a9f40cbfb9d68551cf489460bbb9f224", "language": "R", "lines": 27, "truncated": false, "block": 8, "row": 1654 }, { "path": "RNA_Animal/05.DESeq/02.DESeq_R_AMG.R", "sha256": "9a07aba7af15a53b176a1744586d253dab2762a48e8967e5f4f4eca63340479b", "language": "R", "lines": 53, "truncated": false, "block": 8, "row": 2075 }, { "path": "RNA_Animal/05.DESeq/02.DESeq_R_KAI_IP.R", "sha256": "cd68bdf0e94a14b4d24549efa6cbd73566a71769e32c4eb05619247e6cf7d65c", "language": "R", "lines": 53, "truncated": false, "block": 8, "row": 2059 }, { "path": "RNA_Animal/05.DESeq/02.DESeq_R_KAI_SUB.R", "sha256": "df5d9eaaa34cac1f3fd2158cf51a118236b30d82cb50492321ca3e528eb95f1c", "language": "R", "lines": 52, "truncated": false, "block": 8, "row": 2065 }, { "path": "RNA_Animal/05.DESeq/02.DESeq_R_PILO.R", "sha256": "81dd58f2718ef3f44ac286f3741a4fcd04150ebd304d9712f7097586fa6357d4", "language": "R", "lines": 53, "truncated": false, "block": 8, "row": 2063 }, { "path": "RNA_Animal/05.DESeq/02.DESeq_R_PPS.R", "sha256": "dcfd3e796b511cc6778b71e79157a0908d05bd9a9e16fb26cf38ca115125e2dd", "language": "R", "lines": 73, "truncated": false, "block": 8, "row": 2546 }, { "path": "RNA_Animal/05.DESeq/02.DESeq_R_TBI.R", "sha256": "aa94ed1325e9bdc3a0502438b199b5a26c1188fec85fb16e10f88c14c8f42f57", "language": "R", "lines": 52, "truncated": false, "block": 8, "row": 2068 }, { "path": "RNA_Animal/06.Deconvolution/01.IMPORT_MIXTURE.R", "sha256": "20b836b6fd4d55790aa7a97362e8953353fb7b3d511b0c05991301036668b51d", "language": "R", "lines": 72, "truncated": false, "block": 8, "row": 2422 }, { "path": "RNA_Animal/06.Deconvolution/02.IMPORT_GO.R", "sha256": "cba1c19715a93b63933fc48fbbf9ad0804b55bea762b159d0cbe48c4aa02619e", "language": "R", "lines": 63, "truncated": false, "block": 8, "row": 2260 }, { "path": "RNA_Animal/06.Deconvolution/03.CIBER_01234Docker.sh", "sha256": "7562e46d4af1bef9847aecc8791747246d433ef5f635700b67cfd693047675d7", "language": "Shell", "lines": 118, "truncated": false, "block": 8, "row": 9054 }, { "path": "RNA_Animal/06.Deconvolution/04.CIBER_04HiRes_Merge.R", "sha256": "014ff541c4e6842d5e6260fb5bdb4ac3b136383156a7d32037d1d8242f7cff77", "language": "R", "lines": 75, "truncated": false, "block": 8, "row": 2374 }, { "path": "RNA_Animal/06.Deconvolution/05.DEG_Matrix.R", "sha256": "3a771fd6bd77eed5b6af2bc3d948e52bab371f2a95a8b87569d52ea985a09958", "language": "R", "lines": 87, "truncated": false, "block": 8, "row": 3152 }, { "path": "RNA_Animal/06.Deconvolution/06.DEG_DESeq.R", "sha256": "75a4d6a540fdc2d89e18643e50038fc0105077c4f711f260d5b3b321ab436df3", "language": "R", "lines": 114, "truncated": false, "block": 8, "row": 2948 }, { "path": "RNA_Animal/06.Deconvolution/07.DEG_DESeq_ALL.R", "sha256": "f21c0c7999bc31f13ea1cbe8f55984e36a1167efbea59bafe8d8d00ec81fe4ee", "language": "R", "lines": 32, "truncated": false, "block": 8, "row": 1878 }, { "path": "RNA_Animal/07.Enrichment/GSEA_01.Matrix_GTF_H.R", "sha256": "3d2fe01e3e7df1887a27f9a99602f9c174503cec7a85c0431198c7d3dba80c3e", "language": "R", "lines": 104, "truncated": false, "block": 8, "row": 3140 }, { "path": "RNA_Animal/07.Enrichment/GSEA_02.Matrix_GMT_H.R", "sha256": "8097a326cad48dc33182878fae101c52384612ff46634f6ba545076d61d7bb0c", "language": "R", "lines": 143, "truncated": false, "block": 8, "row": 3568 }, { "path": "RNA_Animal/07.Enrichment/GSEA_03.Matrix_TPM_M_H.R", "sha256": "69d2f853018f48831a0fdf760d387bc9c8e50746604dcf345063a0f180485baf", "language": "R", "lines": 160, "truncated": false, "block": 8, "row": 3895 }, { "path": "RNA_Animal/07.Enrichment/GSEA_03.Matrix_TPM_R_H.R", "sha256": "7251e074008f23a885a7fd54ac6320cd7b0d27bdebc9fdea33c2ec8924ed6d9e", "language": "R", "lines": 99, "truncated": false, "block": 8, "row": 3042 }, { "path": "RNA_Animal/07.Enrichment/GSEA_04.NES_NG.R", "sha256": "79fb50da31caa377124a1c26409f56ad99419fc4c4b98d12aee9da0e2d238d30", "language": "R", "lines": 189, "truncated": false, "block": 8, "row": 3988 }, { "path": "RNA_Animal/07.Enrichment/GSEA_04.NES_NI.R", "sha256": "c3555f3d70168da74af966d2343ef8d3867c3e9ae80cce4d50c97d7b8928f25b", "language": "R", "lines": 180, "truncated": false, "block": 8, "row": 3923 }, { "path": "RNA_Animal/07.Enrichment/GSEA_04.NES_NT_IC.R", "sha256": "e605ced96699db07a72a983cf911f7d6065aacf574f64e266112da69fa34c12f", "language": "R", "lines": 185, "truncated": false, "block": 8, "row": 3979 }, { "path": "RNA_Animal/07.Enrichment/ORA_01.Matrix.R", "sha256": "6802d5d1fddc159f4cdadad07433d27a9a40d243a32a3d63ce32969dd3140341", "language": "R", "lines": 281, "truncated": false, "block": 8, "row": 4568 }, { "path": "RNA_Animal/07.Enrichment/ORA_02.ToppFun.R", "sha256": "b14f2a507a7f7e31d5b306582bebab8bfc136420b3fb27bd0e87639483d81d01", "language": "R", "lines": 92, "truncated": false, "block": 8, "row": 2567 }, { "path": "RNA_Animal/07.Enrichment/ORA_03.ToppFun_category.R", "sha256": "596767eafe3ce884b2ec3b1c0423c0dc1ebcb13e780a249f9bff495da2ae4409", "language": "R", "lines": 310, "truncated": false, "block": 8, "row": 4233 }, { "path": "RNA_Animal/08.Cross_species_gene_comparison/01.Gene_level_comparison_final.R", "sha256": "ec8d68411c6f68ab2def617ce2f99758a2dbccaf38cbaa32a9486b35c3b717f4", "language": "R", "lines": 301, "truncated": false, "block": 8, "row": 4627 }, { "path": "RNA_Animal/08.Cross_species_gene_comparison/02.Dotplot_DEGs.R", "sha256": "b0b3d145eaa8b456f5b729ce13d91ff710a62eb52ad8455d7a1eeb419d4f1335", "language": "R", "lines": 187, "truncated": false, "block": 8, "row": 3937 }, { "path": "RNA_Human/00.Matrix_H.R", "sha256": "e0fc09818671a297bc0fdc5d28b2652e660140647816fed76bf774134b73b170", "language": "R", "lines": 46, "truncated": false, "block": 8, "row": 2462 }, { "path": "RNA_Human/00.Subgrouping_H.R", "sha256": "5315d547df52f448a3fc2609d16aae80265104b47388eaf425aa0e3e3d705f4b", "language": "R", "lines": 100, "truncated": false, "block": 8, "row": 3153 }, { "path": "RNA_Human/01.Pre-processing/03.fastp_paired.sh", "sha256": "ab1764397f6f7632e88662d717c2b1fae4be9b8c4094d9c59945cefefe3de55a", "language": "Shell", "lines": 28, "truncated": false, "block": 8, "row": 7009 }, { "path": "RNA_Human/01.Pre-processing/03.fastp_single.sh", "sha256": "d0c706248ad9d338ea0fd9182809fa4c0bf0b020f101de6c5b32cfdf468254ce", "language": "Shell", "lines": 24, "truncated": false, "block": 8, "row": 6891 }, { "path": "RNA_Human/01.Pre-processing/04.Indexing.sh", "sha256": "e05107911a72f02b1dddce46e113daed8c786f3c7bdf966316e55508adae8c2a", "language": "Shell", "lines": 53, "truncated": false, "block": 8, "row": 7840 }, { "path": "RNA_Human/01.Pre-processing/04.aligned_paired_100.sh", "sha256": "2e8a33e43711d96a2b640cae17ff25a1bdb1497146ff5d4ea385a75ae9057e5a", "language": "Shell", "lines": 39, "truncated": false, "block": 8, "row": 7480 }, { "path": "RNA_Human/01.Pre-processing/04.aligned_paired_125.sh", "sha256": "82c2af641ac46a98802ea98fe2bc3660e4f8aded2a78945c8948c0db9c5f0c14", "language": "Shell", "lines": 40, "truncated": false, "block": 8, "row": 7483 }, { "path": "RNA_Human/01.Pre-processing/04.aligned_paired_150.sh", "sha256": "0e7d91b196a7df2b4ff8aac56405481cf163886a76ad6ae29311c3271da39e64", "language": "Shell", "lines": 39, "truncated": false, "block": 8, "row": 7482 }, { "path": "RNA_Human/01.Pre-processing/04.aligned_single.sh", "sha256": "e57eb9ae084d691c9c9cecd9dff84ffb46fceb96b274320a7b25377252e6c2b6", "language": "Shell", "lines": 38, "truncated": false, "block": 8, "row": 7402 }, { "path": "RNA_Human/02.Quantification/01.HTseq.sh", "sha256": "39873a7c71930d03e387852b856659c49f6c9294f31a6f77baa28d4ac4b367fe", "language": "Shell", "lines": 27, "truncated": false, "block": 8, "row": 6852 }, { "path": "RNA_Human/02.Quantification/02.gtf_table.R", "sha256": "39f389220b92ea2c0442de9a090135145b41fb4df43d907484fc21b609ea16cb", "language": "R", "lines": 36, "truncated": false, "block": 8, "row": 1742 }, { "path": "RNA_Human/02.Quantification/03.Matrix.R", "sha256": "695993d11d54bceeb779976087f29842d1940d040bc354e7b738e433ce7c9efd", "language": "R", "lines": 45, "truncated": false, "block": 8, "row": 2034 }, { "path": "RNA_Human/02.Quantification/04.combat.R", "sha256": "713ad61343c7a85cdf3dfee5280ca982bd553e9d1984b4550cd651d0bc90d837", "language": "R", "lines": 27, "truncated": false, "block": 8, "row": 1746 }, { "path": "RNA_Human/03.Normalization/01.TPM_normalization.R", "sha256": "9516f035000a0fcb1debf66289f1c3d72c10d271c850fbcf33f8965519f9d003", "language": "R", "lines": 16, "truncated": false, "block": 8, "row": 1627 }, { "path": "RNA_Human/04.Clustering/01.Count_PCA.R", "sha256": "4a7276685584b3a2cb852d9f6d4fd5da361f36ce873a220b8b57d8109873c361", "language": "R", "lines": 88, "truncated": false, "block": 8, "row": 2730 }, { "path": "RNA_Human/04.Clustering/02.TPM_PCA.R", "sha256": "da49f61299751998147893f3feb61947a5c5ea3ca58cc7a4591a590709128b58", "language": "R", "lines": 87, "truncated": false, "block": 8, "row": 2713 }, { "path": "RNA_Human/05.Comparison/01.TPM_Comparison.R", "sha256": "6adeca52808cdfc35d12391d569e4f48a4419b38d4518b5cb9f4f5694cdc56cf", "language": "R", "lines": 136, "truncated": false, "block": 8, "row": 3323 }, { "path": "RNA_Human/06.Selection/01.TPM_Outlier_Selection.R", "sha256": "ddc63764a1bf3144677edec773b568117c1d3f5f8ffd57dfb38500de1635ef11", "language": "R", "lines": 189, "truncated": false, "block": 8, "row": 3646 }, { "path": "RNA_Human/06.Selection/02.TPM_Outlier_plot.R", "sha256": "d592e8af4b9425db7837bbb1ad2b4e9735ff4929ddb145d40370bd6eb8544978", "language": "R", "lines": 390, "truncated": false, "block": 8, "row": 4536 }, { "path": "RNA_Human/06.Selection/03.PCA_Outlier_Selection.R", "sha256": "005d57924653efd063c7f397087b48a1ee1526712e2889420c6911d7e09825fa", "language": "R", "lines": 125, "truncated": false, "block": 8, "row": 3228 }, { "path": "RNA_Human/06.Selection/04.PCA_Outlier_plot.R", "sha256": "9af012f1df6e20250cf4ed6cc8a9334a9daf8ccde229664838d6b9bbadf23c86", "language": "R", "lines": 355, "truncated": false, "block": 8, "row": 4458 }, { "path": "RNA_Human/06.Selection/05.TPM_PCA_Outlier_Selection.R", "sha256": "01cc242d53a8c1676ca1f024d822439674dc373048d11d12f0b33531ae617274", "language": "R", "lines": 241, "truncated": false, "block": 8, "row": 3905 }, { "path": "RNA_Human/06.Selection/06.TPM_PCA_Outlier_plot.R", "sha256": "8208f989bd55afe0af3cf0f01b44e8c87ea66abc5d9c4a2f6dec022df0fd9676", "language": "R", "lines": 353, "truncated": false, "block": 8, "row": 4470 }, { "path": "RNA_Human/07.DESeq/01.DESeq.R", "sha256": "62b768688e92df1f80b3c34062d69985fe2612478a9ec363027c9dc623ee08ea", "language": "R", "lines": 55, "truncated": false, "block": 8, "row": 1920 }, { "path": "RNA_Human/07.DESeq/02.DESeq_ALL.R", "sha256": "db1558d6c5ea7dfdf09224a99156e6874d4721fac3f3e559b604dc1651ec26a5", "language": "R", "lines": 26, "truncated": false, "block": 8, "row": 1622 }, { "path": "RNA_Human/08.Enrichment/GSEA_01.Matrix_GTF.R", "sha256": "ef9f1f42cd50a9a4fa15c8ce1e439555119ed5142d1d0a42ccca986ff5137c54", "language": "R", "lines": 56, "truncated": false, "block": 8, "row": 2267 }, { "path": "RNA_Human/08.Enrichment/GSEA_02.Matrix_GMT.R", "sha256": "e03ec4a9b4e0c5117fc31a2fcea4aa942a8d51463de3c0aac867d2ce588d6619", "language": "R", "lines": 78, "truncated": false, "block": 8, "row": 2778 }, { "path": "RNA_Human/08.Enrichment/GSEA_03.Matrix_TPM_hippo.R", "sha256": "5995b71d627f6a58f1f91d52123cf21899419395d0ad93a2ced7ec55ce289513", "language": "R", "lines": 86, "truncated": false, "block": 8, "row": 2845 }, { "path": "RNA_Human/08.Enrichment/GSEA_04.Output_GOBP.R", "sha256": "a011e9119f14a45a81433fabb6ddbac281affc05100c6391e4adf64a521f98d0", "language": "R", "lines": 141, "truncated": false, "block": 8, "row": 3788 }, { "path": "RNA_Human/08.Enrichment/GSEA_05.Output_GOBP_combined.R", "sha256": "5062e5a1d1e1689102b7b10ae2e6967400057c30abdc697f9c2a888411044e3d", "language": "R", "lines": 170, "truncated": false, "block": 8, "row": 3942 }, { "path": "RNA_Human/08.Enrichment/ORA_01.Matrix_DESeq.R", "sha256": "8dea2b170e89ea278b31a0ba37780b133377850eac291c3b0fe303452e906ed9", "language": "R", "lines": 32, "truncated": false, "block": 8, "row": 1826 }, { "path": "RNA_Human/08.Enrichment/ORA_02.ToppFun.R", "sha256": "9ac91095ddff8fd5d299a13071746679e196ced45f7b92425d9339abe36a7c58", "language": "R", "lines": 32, "truncated": false, "block": 8, "row": 1623 }, { "path": "RNA_Human/09.Deconvolution/01.IMPORT_MIXTURE.R", "sha256": "b3e7710a06b752e03110576637617db3e0919ed6637eeb8299dbcf8e409b7f1a", "language": "R", "lines": 48, "truncated": false, "block": 8, "row": 2020 }, { "path": "RNA_Human/09.Deconvolution/02.IMPORT_GO.R", "sha256": "283b51a93f898a29f0dfdf82430508e5deb391acc67f7e9c7c8967a9345eb3e2", "language": "R", "lines": 55, "truncated": false, "block": 8, "row": 2203 }, { "path": "RNA_Human/09.Deconvolution/03.CIBER_01234Docker.sh", "sha256": "82af7b2b6d2c0d56a41e86fdc0dfba4ce085b00dcfbf09674698a1b99f09530a", "language": "Shell", "lines": 91, "truncated": false, "block": 8, "row": 8892 }, { "path": "RNA_Human/09.Deconvolution/04.CIBER_04HiRes_Merge.R", "sha256": "156ed2a72706738fdb1bfb3d8c0630f8e816590a4eb5192a74699e6d135c2e0d", "language": "R", "lines": 52, "truncated": false, "block": 8, "row": 1910 }, { "path": "RNA_Human/09.Deconvolution/05.DEG_Matrix_Integ.R", "sha256": "e76a80a8d1bd1b718b04926740403354ae2c60b51d8e47ea218ad9c906709ca7", "language": "R", "lines": 31, "truncated": false, "block": 8, "row": 1579 }, { "path": "RNA_Human/09.Deconvolution/06.DEG_DESeq_Integ.R", "sha256": "6dbf34ffa48a30abed9371bd70cd42979d03b54f26b114d18e0bb0a36487176b", "language": "R", "lines": 38, "truncated": false, "block": 8, "row": 1660 }, { "path": "RNA_Human/09.Deconvolution/07.DEG_DESeq_ALL_Integ.R", "sha256": "218421af0d5684bc935e1337f72b00fe86984ddfd704178cc43beaad5f9acee1", "language": "R", "lines": 43, "truncated": false, "block": 8, "row": 2054 }, { "path": "RNA_Human/09.Deconvolution/08.Correlation_Celltype.R", "sha256": "0b35db8c2ffbc2545b8d051e047c3d66ac43523ad894f340454c564d3a4aafbe", "language": "R", "lines": 114, "truncated": false, "block": 8, "row": 3445 }, { "path": "RNA_Human/10.Correlation/01.Correlation_Epileptogenesis.R", "sha256": "bd339bc20110114bc14337825b98d10467917dd375fc33c96b3b00844c2ec14a", "language": "R", "lines": 249, "truncated": false, "block": 8, "row": 4355 }, { "path": "RNA_Human/10.Correlation/01.Correlation_WholeGene.R", "sha256": "86c92cba3032c07a34475ab89e10877fdf1904142d3c540ef939876545da88af", "language": "R", "lines": 244, "truncated": false, "block": 8, "row": 4325 }, { "path": "RNA_Human/10.Correlation/02.Dotplot_correlation_Epileptogenesis.R", "sha256": "5d9cbee54c363fe08d6e3f3382793219f37ab2580091c326535c95d0069372ef", "language": "R", "lines": 336, "truncated": false, "block": 8, "row": 4632 }, { "path": "RNA_Human/10.Correlation/02.Dotplot_correlation_Epileptogenesis_phase.R", "sha256": "4a5c02ae36a2074ebe53551e96826ef9e9f27f9e4bc5e2ea1b43b15e56c70a0e", "language": "R", "lines": 225, "truncated": false, "block": 8, "row": 4183 }, { "path": "RNA_Human/10.Correlation/02.Dotplot_correlation_WholeGene.R", "sha256": "a7acb25cf3a02e7e4d3fdfd1e035e1941fe5c335d29d23ee0bad3d655712b4fe", "language": "R", "lines": 329, "truncated": false, "block": 8, "row": 4612 }, { "path": "RNA_Human/10.Correlation/02.Dotplot_correlation_WholeGene_phase.R", "sha256": "b4bbf4e4e6a065738dfb3449146f84d65b6671cf494e6352f295eaf23e9f4549", "language": "R", "lines": 210, "truncated": false, "block": 8, "row": 4092 }, { "path": "RNA_Human/10.Correlation/03.Dotplot_shared_genes_Epileptogenesis.R", "sha256": "b99379b312b9612c72bd79d8f25c09a5a73fa31da38565c7c67a418d61e28203", "language": "R", "lines": 305, "truncated": false, "block": 8, "row": 4530 }, { "path": "RNA_Human/10.Correlation/03.Dotplot_shared_genes_WholeGene.R", "sha256": "f3a65ded8339a0f3edb2ff57330efae4bef27de9f4e347d8219295ad5a747b0a", "language": "R", "lines": 302, "truncated": false, "block": 8, "row": 4492 }, { "path": "RNA_Human/10.Correlation/04.Celltype_Corr_Matrix_Epileptogenesis.R", "sha256": "1554848df989b12b37c371e5d5c2e36ec712d86ac77651c142deb5949b1cce57", "language": "R", "lines": 99, "truncated": false, "block": 8, "row": 3189 }, { "path": "RNA_Human/10.Correlation/04.Celltype_Corr_Matrix_WholeGene.R", "sha256": "6e6798091e6fd9a84727f5c399848a6ae05264db95f9023991f0a91be913f0c7", "language": "R", "lines": 89, "truncated": false, "block": 8, "row": 3111 }, { "path": "RNA_Human/10.Correlation/04.Dotplot_Celltype_Epileptogenesis.R", "sha256": "672ae56640ab25a89a803531da6c4e59ee5459384fa16c42c51c5c03d90354b4", "language": "R", "lines": 154, "truncated": false, "block": 8, "row": 3847 }, { "path": "RNA_Human/10.Correlation/04.Dotplot_Celltype_WholeGene.R", "sha256": "3294bb3acf9926c96b2f1160d15e6998103f6d690ed07a4480f932faa8182606", "language": "R", "lines": 150, "truncated": false, "block": 8, "row": 3748 }, { "path": "RNA_Human/10.Correlation/05.GO_Corr_Matrix.R", "sha256": "50d87f6f2786b2055348fe43ffd3197e95d8e93c3e2806c4bc3c65c640b8046b", "language": "R", "lines": 132, "truncated": false, "block": 8, "row": 3585 }, { "path": "RNA_Human/10.Correlation/05.GO_Dotplot.R", "sha256": "3e7fbc513d7f5ceb8562852e0acd47290e0398725160fbf47cb268314052d229", "language": "R", "lines": 153, "truncated": false, "block": 8, "row": 3817 }, { "path": "RNA_Human/11.Sample_variables/00.sankey_plot.R", "sha256": "c4a882cb2e0adc279e1e77bb23bb4aa7dbd25b236668eec3234e6d62f7fcacf2", "language": "R", "lines": 57, "truncated": false, "block": 8, "row": 2139 }, { "path": "RNA_Human/11.Sample_variables/01.matrix.R", "sha256": "48ce07ef5b9887821843e543a140812cbc7049efd070ce0d284cf232e81deba5", "language": "R", "lines": 49, "truncated": false, "block": 8, "row": 2159 }, { "path": "RNA_Human/11.Sample_variables/02.deseq.R", "sha256": "ae2b4666da4a6c6980c3bd390d0c7717e644ea72052c312403b86c83f83b310b", "language": "R", "lines": 63, "truncated": false, "block": 8, "row": 2259 }, { "path": "RNA_Human/11.Sample_variables/02.deseq_ALL.R", "sha256": "40f9dcc608a5d682f077aae512f4e5742f244abd62d88cf4e4d1c1120a224e02", "language": "R", "lines": 52, "truncated": false, "block": 8, "row": 2249 }, { "path": "RNA_Human/11.Sample_variables/03.correlation.R", "sha256": "07ba91d3ca5a417eecae2789114cd29e9d84d1d15b35fd523e974d9216bd6781", "language": "R", "lines": 299, "truncated": false, "block": 8, "row": 4520 }, { "path": "RNA_Human/11.Sample_variables/04.correlation_additional.R", "sha256": "53c683fd2a6e88c3fd875e866fd226a3c85bae7adc818136ff2f15766c65fd67", "language": "R", "lines": 348, "truncated": false, "block": 8, "row": 4666 }, { "path": "Scratch_settings.sh", "sha256": "a387a9896a98ecf87d25e2f929afe298ad58e9a8aed2b9592b9a15de963c5d37", "language": "Shell", "lines": 210, "truncated": false, "block": 8, "row": 9288 }, { "path": "scRNA_Animal/01.GSE185862_10X_Deconv.ipynb", "sha256": "8af4b7b2abf206061c4fbd8a1fcbf5ad8d96131223eb2843adbbf7c8a156ed70", "language": "Jupyter", "lines": 618, "truncated": false, "block": 6, "row": 896 }, { "path": "scRNA_Animal/02.GSE185862_10X_Deconv_OPC.ipynb", "sha256": "dfd25f8f1f5ac7c2994cccd93bc2e23adce9dadb2bdc6c41b0f6470761a16c27", "language": "Jupyter", "lines": 685, "truncated": false, "block": 6, "row": 931 }, { "path": "scRNA_Animal/03.GSE185862_10X_Deconv_plot.ipynb", "sha256": "717f2012ce26dd41e4d4e00b77f2eeaf6c3f779a2968ec97c4b19a8be970edcc", "language": "Jupyter", "lines": 185, "truncated": false, "block": 5, "row": 17234 }, { "path": "scRNA_Human/01.H_GSE160189_Seurat.R", "sha256": "b75cdb15740bb445bf3da4875c53a7758d081febcd77dda0e0c088d3a612923e", "language": "R", "lines": 55, "truncated": false, "block": 8, "row": 2078 }, { "path": "scRNA_Human/01.H_GSE186538_Seurat.R", "sha256": "88cb278c45264c07b85509f173921ee181060533567babddc528ae8e7bd3cb23", "language": "R", "lines": 90, "truncated": false, "block": 8, "row": 3139 }, { "path": "scRNA_Human/02.Integ_2_RPCA.R", "sha256": "c3560f009a62223eac86bb6f3480d2ff5d1722689beb659b76dab43c9e9ae5f3", "language": "R", "lines": 118, "truncated": false, "block": 8, "row": 3491 }, { "path": "scRNA_Human/03.Integ_2_Deconv_Sig_DEG.R", "sha256": "7723c4e1b78c8ff38047130e492b362001ef8b155e68408a51317e1cf21b6628", "language": "R", "lines": 95, "truncated": false, "block": 8, "row": 3148 }, { "path": "scRNA_Human/04.Integ_2_Validation_AvgEpr.R", "sha256": "807e89816a68595b5e88f19bb2fb5d15da344996ac24ac0ff4777f4a63aceb51", "language": "R", "lines": 101, "truncated": false, "block": 8, "row": 2644 }, { "path": "scRNA_Human/05.Integ_2_Validation_Pseudobulk.R", "sha256": "eed581d74ced10388345567f10596b3edc3bc18da005aa5f5b9415082f0a5466", "language": "R", "lines": 207, "truncated": false, "block": 8, "row": 3713 } ] }