diff --git a/nbs/05_preprocessing/00-gtex_v8-split_by_tissue.ipynb b/nbs/05_preprocessing/00-gtex_v8-split_by_tissue.ipynb index 5251e9bf..29ee3dd5 100644 --- a/nbs/05_preprocessing/00-gtex_v8-split_by_tissue.ipynb +++ b/nbs/05_preprocessing/00-gtex_v8-split_by_tissue.ipynb @@ -5,10 +5,10 @@ "id": "871d5ed2-95c8-48db-b3b3-394fea7a035b", "metadata": { "papermill": { - "duration": 0.071341, - "end_time": "2022-01-21T04:29:15.960721", + "duration": 0.006825, + "end_time": "2023-09-06T21:15:02.890652", "exception": false, - "start_time": "2022-01-21T04:29:15.889380", + "start_time": "2023-09-06T21:15:02.883827", "status": "completed" }, "tags": [] @@ -22,10 +22,10 @@ "id": "06b29f41-a8f0-4274-8f72-a5b7cc19bc4e", "metadata": { "papermill": { - "duration": 0.034925, - "end_time": "2022-01-21T04:29:16.030759", + "duration": 0.006827, + "end_time": "2023-09-06T21:15:02.907512", "exception": false, - "start_time": "2022-01-21T04:29:15.995834", + "start_time": "2023-09-06T21:15:02.900685", "status": "completed" }, "tags": [] @@ -39,10 +39,10 @@ "id": "d05acbf3-ee34-4e31-b359-58d5ffde4213", "metadata": { "papermill": { - 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" Pandas(gene_ens_id='ENSG00000254158.1', gene_symbol='RP11-281O15.5'),\n", - " Pandas(gene_ens_id='ENSG00000254101.5', gene_symbol='LINC02055')]" + "[Pandas(gene_ens_id='ENSG00000177447.6', gene_symbol='CBX3P1'),\n", + " Pandas(gene_ens_id='ENSG00000244034.3', gene_symbol='RN7SL424P'),\n", + " Pandas(gene_ens_id='ENSG00000255205.1', gene_symbol='MED28P5'),\n", + " Pandas(gene_ens_id='ENSG00000137880.5', gene_symbol='GCHFR'),\n", + " Pandas(gene_ens_id='ENSG00000229087.1', gene_symbol='RP11-32P22.1')]" ] }, "execution_count": 22, @@ -1625,16 +1625,16 @@ "id": "c59f8fb5-50aa-4d8d-8fa1-e49b79575eff", "metadata": { "execution": { - "iopub.execute_input": "2022-01-21T05:17:08.302697Z", - "iopub.status.busy": "2022-01-21T05:17:08.287182Z", - "iopub.status.idle": "2022-01-21T05:17:08.308550Z", - "shell.execute_reply": "2022-01-21T05:17:08.309012Z" + "iopub.execute_input": "2023-09-06T21:37:59.308332Z", + "iopub.status.busy": "2023-09-06T21:37:59.308240Z", + "iopub.status.idle": "2023-09-06T21:37:59.320386Z", + "shell.execute_reply": "2023-09-06T21:37:59.320207Z" }, "papermill": { - 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" ENSG00000115944.14\n", - " COX7A2L\n", + " ENSG00000255205.1\n", + " MED28P5\n", " \n", " \n", " 3\n", - " ENSG00000254158.1\n", - " RP11-281O15.5\n", + " ENSG00000137880.5\n", + " GCHFR\n", " \n", " \n", " 4\n", - " ENSG00000254101.5\n", - " LINC02055\n", + " ENSG00000229087.1\n", + " RP11-32P22.1\n", " \n", " \n", "\n", "" ], "text/plain": [ - " gene_ens_id gene_symbol\n", - "0 ENSG00000222320.1 RNU6-1050P\n", - "1 ENSG00000200554.1 RNU6-1020P\n", - "2 ENSG00000115944.14 COX7A2L\n", - "3 ENSG00000254158.1 RP11-281O15.5\n", - "4 ENSG00000254101.5 LINC02055" + " gene_ens_id gene_symbol\n", + "0 ENSG00000177447.6 CBX3P1\n", + "1 ENSG00000244034.3 RN7SL424P\n", + "2 ENSG00000255205.1 MED28P5\n", + "3 ENSG00000137880.5 GCHFR\n", + "4 ENSG00000229087.1 RP11-32P22.1" ] }, "execution_count": 25, @@ -1779,10 +1779,10 @@ "id": "90a5f71f-5f39-4d9c-b6c8-487a0b487aea", "metadata": { "papermill": { - "duration": 0.068817, - "end_time": "2022-01-21T05:17:08.773802", + "duration": 0.004561, + "end_time": "2023-09-06T21:37:59.354566", "exception": false, - 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"shell.execute_reply": "2022-01-21T05:17:10.181784Z" + "iopub.execute_input": "2023-09-06T21:37:59.490998Z", + "iopub.status.busy": "2023-09-06T21:37:59.490906Z", + "iopub.status.idle": "2023-09-06T21:37:59.494387Z", + "shell.execute_reply": "2023-09-06T21:37:59.494259Z" }, "papermill": { - "duration": 0.080601, - "end_time": "2022-01-21T05:17:10.182330", + "duration": 0.008895, + "end_time": "2023-09-06T21:37:59.494925", "exception": false, - "start_time": "2022-01-21T05:17:10.101729", + "start_time": "2023-09-06T21:37:59.486030", "status": "completed" }, "tags": [] @@ -2061,31 +2061,31 @@ " \n", " \n", " 0\n", - " ENSG00000222320.1\n", - " RNU6-1050P\n", + " ENSG00000177447.6\n", + " CBX3P1\n", " 17\n", - " 10\n", + " 6\n", " \n", " \n", - " 2\n", - " ENSG00000115944.14\n", - " COX7A2L\n", + " 5\n", + " ENSG00000139370.11\n", + " SLC15A4\n", " 18\n", " 7\n", " \n", " \n", - " 1432\n", - " ENSG00000229232.6_PAR_Y\n", - " KRT18P53\n", + " 88\n", + " ENSG00000237040.6_PAR_Y\n", + " DPH3P2\n", " 23\n", - " 8\n", + " 6\n", " \n", " \n", - " 3780\n", - " ENSG00000182378.13_PAR_Y\n", - " PLCXD1\n", + " 6323\n", + " ENSG00000214717.11_PAR_Y\n", + " ZBED1\n", " 24\n", - " 6\n", + " 5\n", " \n", " \n", "\n", @@ -2093,10 +2093,10 @@ ], "text/plain": [ " gene_ens_id gene_symbol id_len symbol_len\n", - "0 ENSG00000222320.1 RNU6-1050P 17 10\n", - "2 ENSG00000115944.14 COX7A2L 18 7\n", - "1432 ENSG00000229232.6_PAR_Y KRT18P53 23 8\n", - "3780 ENSG00000182378.13_PAR_Y PLCXD1 24 6" + "0 ENSG00000177447.6 CBX3P1 17 6\n", + "5 ENSG00000139370.11 SLC15A4 18 7\n", + "88 ENSG00000237040.6_PAR_Y DPH3P2 23 6\n", + "6323 ENSG00000214717.11_PAR_Y ZBED1 24 5" ] }, "execution_count": 33, @@ -2113,10 +2113,10 @@ "id": "e5891b45-ff1b-45c8-a1d7-776afcf7d3de", "metadata": { "papermill": { - "duration": 0.069583, - "end_time": "2022-01-21T05:17:10.321445", + "duration": 0.004697, + "end_time": "2023-09-06T21:37:59.504355", "exception": false, - "start_time": "2022-01-21T05:17:10.251862", + "start_time": "2023-09-06T21:37:59.499658", "status": "completed" }, "tags": [] @@ -2131,16 +2131,16 @@ "id": "a6ed0534-8313-46e8-a6ad-e52137ce84c7", "metadata": { "execution": { - 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"shell.execute_reply": "2022-01-21T05:17:11.199074Z" + "iopub.execute_input": "2023-09-06T21:37:59.570139Z", + "iopub.status.busy": "2023-09-06T21:37:59.570035Z", + "iopub.status.idle": "2023-09-06T21:37:59.573751Z", + "shell.execute_reply": "2023-09-06T21:37:59.573629Z" }, "papermill": { - "duration": 0.082726, - "end_time": "2022-01-21T05:17:11.199189", + "duration": 0.00924, + "end_time": "2023-09-06T21:37:59.574315", "exception": false, - "start_time": "2022-01-21T05:17:11.116463", + "start_time": "2023-09-06T21:37:59.565075", "status": "completed" }, "tags": [] @@ -2305,135 +2305,135 @@ " \n", " \n", " \n", - " 6363\n", + " 55047\n", " ENSG00000164458.9\n", " T\n", " 17\n", " 1\n", " \n", " \n", - " 633\n", - " ENSG00000201368.2\n", + " 613\n", + " ENSG00000212479.2\n", " U3\n", " 17\n", " 2\n", " \n", " \n", - " 39\n", - " ENSG00000109072.13\n", - " VTN\n", + " 192\n", + " ENSG00000148180.19\n", + " GSN\n", " 18\n", " 3\n", " \n", " \n", - " 38\n", - " ENSG00000138768.14\n", - " USO1\n", + " 22\n", + " ENSG00000021826.14\n", + " CPS1\n", " 18\n", " 4\n", " \n", " \n", - " 8\n", - " ENSG00000184730.10\n", - " APOBR\n", - " 18\n", + " 3\n", + " ENSG00000137880.5\n", + " GCHFR\n", + " 17\n", " 5\n", " \n", " \n", - " 9\n", - " ENSG00000232991.5\n", - " GACAT1\n", + " 0\n", + " ENSG00000177447.6\n", + " CBX3P1\n", " 17\n", " 6\n", " \n", " \n", " 2\n", - " ENSG00000115944.14\n", - " COX7A2L\n", - " 18\n", + " ENSG00000255205.1\n", + " MED28P5\n", + " 17\n", " 7\n", " \n", " \n", " 17\n", - " ENSG00000271638.1\n", - " BNIP3P19\n", + " ENSG00000236830.6\n", + " CBR3-AS1\n", " 17\n", " 8\n", " \n", " \n", - " 4\n", - " ENSG00000254101.5\n", - " LINC02055\n", + " 1\n", + " ENSG00000244034.3\n", + " RN7SL424P\n", " 17\n", " 9\n", " \n", " \n", - " 0\n", - " ENSG00000222320.1\n", - " RNU6-1050P\n", + " 29\n", + " ENSG00000276728.1\n", + " AC142472.6\n", " 17\n", " 10\n", " \n", " \n", - " 43\n", - " ENSG00000236641.1\n", - " CTA-221G9.7\n", + " 16\n", + " ENSG00000258557.1\n", + " AE000659.41\n", " 17\n", " 11\n", " \n", " \n", - " 10\n", - " ENSG00000258410.1\n", - " RP11-173D3.1\n", + " 4\n", + " ENSG00000229087.1\n", + " RP11-32P22.1\n", " 17\n", " 12\n", " \n", " \n", - " 3\n", - " ENSG00000254158.1\n", - " RP11-281O15.5\n", + " 8\n", + " ENSG00000243894.1\n", + " RP11-489M13.1\n", " 17\n", " 13\n", " \n", " \n", - " 217\n", - " ENSG00000254510.1\n", - " RP11-867G23.10\n", + " 75\n", + " ENSG00000282772.1\n", + " RP11-753C18.12\n", " 17\n", " 14\n", " \n", " \n", - " 69\n", + " 501\n", " ENSG00000249923.1\n", " XXbac-B444P24.8\n", " 17\n", " 15\n", " \n", " \n", - " 1509\n", - " ENSG00000233085.5\n", - " XXyac-YX65C7_A.3\n", + " 2309\n", + " ENSG00000278657.1\n", + " LL22NC03-23C6.13\n", " 17\n", " 16\n", " \n", " \n", - " 895\n", - " ENSG00000277427.1\n", - " XXbac-BPG154L12.5\n", + " 1278\n", + " ENSG00000227206.1\n", + " XXbac-BCX196D17.5\n", " 17\n", " 17\n", " \n", " \n", - " 690\n", - " ENSG00000270896.1\n", - " XXbac-BPG170G13.31\n", + " 1074\n", + " ENSG00000272217.1\n", + " XXbac-BPG157A10.21\n", " 17\n", " 18\n", " \n", " \n", - " 573\n", - " ENSG00000270935.1\n", - " XXbac-BPGBPG24O18.1\n", + " 2760\n", + " ENSG00000272316.1\n", + " XXbac-BPGBPG55C20.2\n", " 17\n", " 19\n", " \n", @@ -2442,26 +2442,26 @@ "" ], "text/plain": [ - " gene_ens_id gene_symbol id_len symbol_len\n", - "6363 ENSG00000164458.9 T 17 1\n", - "633 ENSG00000201368.2 U3 17 2\n", - "39 ENSG00000109072.13 VTN 18 3\n", - "38 ENSG00000138768.14 USO1 18 4\n", - "8 ENSG00000184730.10 APOBR 18 5\n", - "9 ENSG00000232991.5 GACAT1 17 6\n", - "2 ENSG00000115944.14 COX7A2L 18 7\n", - "17 ENSG00000271638.1 BNIP3P19 17 8\n", - "4 ENSG00000254101.5 LINC02055 17 9\n", - "0 ENSG00000222320.1 RNU6-1050P 17 10\n", - "43 ENSG00000236641.1 CTA-221G9.7 17 11\n", - "10 ENSG00000258410.1 RP11-173D3.1 17 12\n", - "3 ENSG00000254158.1 RP11-281O15.5 17 13\n", - "217 ENSG00000254510.1 RP11-867G23.10 17 14\n", - "69 ENSG00000249923.1 XXbac-B444P24.8 17 15\n", - "1509 ENSG00000233085.5 XXyac-YX65C7_A.3 17 16\n", - "895 ENSG00000277427.1 XXbac-BPG154L12.5 17 17\n", - "690 ENSG00000270896.1 XXbac-BPG170G13.31 17 18\n", - "573 ENSG00000270935.1 XXbac-BPGBPG24O18.1 17 19" + " gene_ens_id gene_symbol id_len symbol_len\n", + "55047 ENSG00000164458.9 T 17 1\n", + "613 ENSG00000212479.2 U3 17 2\n", + "192 ENSG00000148180.19 GSN 18 3\n", + "22 ENSG00000021826.14 CPS1 18 4\n", + "3 ENSG00000137880.5 GCHFR 17 5\n", + "0 ENSG00000177447.6 CBX3P1 17 6\n", + "2 ENSG00000255205.1 MED28P5 17 7\n", + "17 ENSG00000236830.6 CBR3-AS1 17 8\n", + "1 ENSG00000244034.3 RN7SL424P 17 9\n", + "29 ENSG00000276728.1 AC142472.6 17 10\n", + "16 ENSG00000258557.1 AE000659.41 17 11\n", + "4 ENSG00000229087.1 RP11-32P22.1 17 12\n", + "8 ENSG00000243894.1 RP11-489M13.1 17 13\n", + "75 ENSG00000282772.1 RP11-753C18.12 17 14\n", + "501 ENSG00000249923.1 XXbac-B444P24.8 17 15\n", + "2309 ENSG00000278657.1 LL22NC03-23C6.13 17 16\n", + "1278 ENSG00000227206.1 XXbac-BCX196D17.5 17 17\n", + "1074 ENSG00000272217.1 XXbac-BPG157A10.21 17 18\n", + "2760 ENSG00000272316.1 XXbac-BPGBPG55C20.2 17 19" ] }, "execution_count": 38, @@ -2479,10 +2479,10 @@ "id": "2302ba84-1dde-4949-92d2-bf036f934717", "metadata": { "papermill": { - "duration": 0.070099, - "end_time": "2022-01-21T05:17:11.340166", + "duration": 0.004764, + "end_time": "2023-09-06T21:37:59.583994", "exception": false, - "start_time": "2022-01-21T05:17:11.270067", + "start_time": "2023-09-06T21:37:59.579230", "status": "completed" }, "tags": [] @@ -2497,16 +2497,16 @@ "id": "3dc54ed8-52a2-4075-b9c3-261c612919fa", "metadata": { "execution": { - "iopub.execute_input": "2022-01-21T05:17:11.487633Z", - "iopub.status.busy": "2022-01-21T05:17:11.487177Z", - "iopub.status.idle": "2022-01-21T05:17:11.494585Z", - "shell.execute_reply": "2022-01-21T05:17:11.494166Z" + "iopub.execute_input": "2023-09-06T21:37:59.594322Z", + "iopub.status.busy": "2023-09-06T21:37:59.594058Z", + "iopub.status.idle": "2023-09-06T21:37:59.598463Z", + "shell.execute_reply": "2023-09-06T21:37:59.598326Z" }, "papermill": { - "duration": 0.083657, - "end_time": "2022-01-21T05:17:11.494682", + "duration": 0.01012, + "end_time": "2023-09-06T21:37:59.598959", "exception": false, - "start_time": "2022-01-21T05:17:11.411025", + "start_time": "2023-09-06T21:37:59.588839", "status": "completed" }, "tags": [] @@ -2522,16 +2522,16 @@ "id": "4682c165-5719-41d7-8e0a-4a833f3567ce", "metadata": { "execution": { - "iopub.execute_input": "2022-01-21T05:17:11.642507Z", - "iopub.status.busy": "2022-01-21T05:17:11.642055Z", - "iopub.status.idle": "2022-01-21T05:17:11.658740Z", - "shell.execute_reply": "2022-01-21T05:17:11.658321Z" + "iopub.execute_input": "2023-09-06T21:37:59.609071Z", + "iopub.status.busy": "2023-09-06T21:37:59.609004Z", + "iopub.status.idle": "2023-09-06T21:37:59.615939Z", + "shell.execute_reply": "2023-09-06T21:37:59.615794Z" }, "papermill": { - "duration": 0.093848, - "end_time": "2022-01-21T05:17:11.658850", + "duration": 0.012643, + "end_time": "2023-09-06T21:37:59.616494", "exception": false, - "start_time": "2022-01-21T05:17:11.565002", + "start_time": "2023-09-06T21:37:59.603851", "status": "completed" }, "tags": [] @@ -2559,16 +2559,16 @@ "id": "16f7d4c6-5514-4db3-88e5-7969ced73e56", "metadata": { "execution": { - "iopub.execute_input": "2022-01-21T05:17:11.811346Z", - "iopub.status.busy": "2022-01-21T05:17:11.810791Z", - "iopub.status.idle": "2022-01-21T05:17:11.820002Z", - "shell.execute_reply": "2022-01-21T05:17:11.819505Z" + "iopub.execute_input": "2023-09-06T21:37:59.626940Z", + "iopub.status.busy": "2023-09-06T21:37:59.626817Z", + "iopub.status.idle": "2023-09-06T21:37:59.632887Z", + "shell.execute_reply": "2023-09-06T21:37:59.632758Z" }, "papermill": { - "duration": 0.088583, - "end_time": "2022-01-21T05:17:11.820097", + "duration": 0.011833, + "end_time": "2023-09-06T21:37:59.633343", "exception": false, - "start_time": "2022-01-21T05:17:11.731514", + "start_time": "2023-09-06T21:37:59.621510", "status": "completed" }, "tags": [] @@ -2601,28 +2601,28 @@ " \n", " \n", " \n", - " 56122\n", - " ENSG00000275305.1\n", + " 36856\n", + " ENSG00000201285.1\n", " 5S_rRNA\n", " \n", " \n", - " 49672\n", - " ENSG00000274097.1\n", + " 1651\n", + " ENSG00000275305.1\n", " 5S_rRNA\n", " \n", " \n", - " 49571\n", - " ENSG00000274059.1\n", + " 51167\n", + " ENSG00000277488.1\n", " 5S_rRNA\n", " \n", " \n", - " 4303\n", - " ENSG00000277411.1\n", + " 16989\n", + " ENSG00000277418.1\n", " 5S_rRNA\n", " \n", " \n", - " 32225\n", - " ENSG00000212595.1\n", + " 46837\n", + " ENSG00000277049.1\n", " 5S_rRNA\n", " \n", " \n", @@ -2631,28 +2631,28 @@ " ...\n", " \n", " \n", - " 52200\n", - " ENSG00000275939.1\n", + " 31958\n", + " ENSG00000277306.1\n", " uc_338\n", " \n", " \n", - " 2260\n", - " ENSG00000274845.1\n", + " 10036\n", + " ENSG00000278498.1\n", " uc_338\n", " \n", " \n", - " 881\n", - " ENSG00000278236.1\n", + " 14278\n", + " ENSG00000277916.1\n", " uc_338\n", " \n", " \n", - " 17000\n", - " ENSG00000278218.1\n", + " 51878\n", + " ENSG00000275414.1\n", " uc_338\n", " \n", " \n", - " 30028\n", - " ENSG00000274127.1\n", + " 56195\n", + " ENSG00000278587.1\n", " uc_338\n", " \n", " \n", @@ -2662,17 +2662,17 @@ ], "text/plain": [ " gene_ens_id gene_symbol\n", - "56122 ENSG00000275305.1 5S_rRNA\n", - "49672 ENSG00000274097.1 5S_rRNA\n", - "49571 ENSG00000274059.1 5S_rRNA\n", - "4303 ENSG00000277411.1 5S_rRNA\n", - "32225 ENSG00000212595.1 5S_rRNA\n", + "36856 ENSG00000201285.1 5S_rRNA\n", + "1651 ENSG00000275305.1 5S_rRNA\n", + "51167 ENSG00000277488.1 5S_rRNA\n", + "16989 ENSG00000277418.1 5S_rRNA\n", + "46837 ENSG00000277049.1 5S_rRNA\n", "... ... ...\n", - "52200 ENSG00000275939.1 uc_338\n", - "2260 ENSG00000274845.1 uc_338\n", - "881 ENSG00000278236.1 uc_338\n", - "17000 ENSG00000278218.1 uc_338\n", - "30028 ENSG00000274127.1 uc_338\n", + "31958 ENSG00000277306.1 uc_338\n", + "10036 ENSG00000278498.1 uc_338\n", + "14278 ENSG00000277916.1 uc_338\n", + "51878 ENSG00000275414.1 uc_338\n", + "56195 ENSG00000278587.1 uc_338\n", "\n", "[1807 rows x 2 columns]" ] @@ -2695,16 +2695,16 @@ "id": "a439d27f-6ae4-47ce-bd89-0d5bb2100f7d", "metadata": { "execution": { - "iopub.execute_input": "2022-01-21T05:17:11.970134Z", - "iopub.status.busy": "2022-01-21T05:17:11.967137Z", - "iopub.status.idle": "2022-01-21T05:17:11.972209Z", - "shell.execute_reply": "2022-01-21T05:17:11.972553Z" + "iopub.execute_input": "2023-09-06T21:37:59.643681Z", + "iopub.status.busy": "2023-09-06T21:37:59.643565Z", + "iopub.status.idle": "2023-09-06T21:37:59.646092Z", + "shell.execute_reply": "2023-09-06T21:37:59.645776Z" }, "papermill": { - "duration": 0.080191, - "end_time": "2022-01-21T05:17:11.972675", + "duration": 0.008219, + "end_time": "2023-09-06T21:37:59.646665", "exception": false, - "start_time": "2022-01-21T05:17:11.892484", + "start_time": "2023-09-06T21:37:59.638446", "status": "completed" }, "tags": [] @@ -2720,16 +2720,16 @@ "id": "78f3b40d-a624-4c17-9c01-f339cd09c8d9", "metadata": { "execution": { - "iopub.execute_input": "2022-01-21T05:17:12.124801Z", - "iopub.status.busy": "2022-01-21T05:17:12.124196Z", - "iopub.status.idle": "2022-01-21T05:17:12.126793Z", - "shell.execute_reply": "2022-01-21T05:17:12.126410Z" + "iopub.execute_input": "2023-09-06T21:37:59.657334Z", + "iopub.status.busy": "2023-09-06T21:37:59.657239Z", + "iopub.status.idle": "2023-09-06T21:37:59.661581Z", + "shell.execute_reply": "2023-09-06T21:37:59.661448Z" }, "papermill": { - "duration": 0.082244, - "end_time": "2022-01-21T05:17:12.126890", + "duration": 0.010125, + "end_time": "2023-09-06T21:37:59.661965", "exception": false, - "start_time": "2022-01-21T05:17:12.044646", + "start_time": "2023-09-06T21:37:59.651840", "status": "completed" }, "tags": [] @@ -2748,10 +2748,10 @@ "id": "03747a27-4636-48e5-8c1f-3a75fc174a4d", "metadata": { "papermill": { - 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"shell.execute_reply": "2022-01-21T05:23:06.138828Z" + "iopub.execute_input": "2023-09-06T21:39:55.018858Z", + "iopub.status.busy": "2023-09-06T21:39:55.018784Z", + "iopub.status.idle": "2023-09-06T21:39:55.021142Z", + "shell.execute_reply": "2023-09-06T21:39:55.020967Z" }, "papermill": { - "duration": 0.131395, - "end_time": "2022-01-21T05:23:06.139351", + "duration": 0.016767, + "end_time": "2023-09-06T21:39:55.021624", "exception": false, - "start_time": "2022-01-21T05:23:06.007956", + "start_time": "2023-09-06T21:39:55.004857", "status": "completed" }, "tags": [] @@ -4724,16 +4724,16 @@ "id": "517e0521-2b48-4b44-8ab0-03b61faaf043", "metadata": { "execution": { - "iopub.execute_input": "2022-01-21T05:23:06.400795Z", - "iopub.status.busy": "2022-01-21T05:23:06.400251Z", - "iopub.status.idle": "2022-01-21T05:23:06.402684Z", - "shell.execute_reply": "2022-01-21T05:23:06.403066Z" + "iopub.execute_input": "2023-09-06T21:39:55.048652Z", + "iopub.status.busy": "2023-09-06T21:39:55.048569Z", + "iopub.status.idle": "2023-09-06T21:39:55.053270Z", + "shell.execute_reply": "2023-09-06T21:39:55.053093Z" }, "papermill": { - "duration": 0.138424, - "end_time": "2022-01-21T05:23:06.403182", + "duration": 0.018889, + "end_time": "2023-09-06T21:39:55.053754", "exception": false, - "start_time": "2022-01-21T05:23:06.264758", + "start_time": "2023-09-06T21:39:55.034865", "status": "completed" }, "tags": [] @@ -4881,16 +4881,16 @@ "id": "754a2538-7988-40c6-b197-c5c0e4327350", "metadata": { "execution": { - "iopub.execute_input": "2022-01-21T05:23:06.658741Z", - "iopub.status.busy": "2022-01-21T05:23:06.658271Z", - "iopub.status.idle": "2022-01-21T05:23:06.688356Z", - "shell.execute_reply": "2022-01-21T05:23:06.687892Z" + "iopub.execute_input": "2023-09-06T21:39:55.080729Z", + "iopub.status.busy": "2023-09-06T21:39:55.080641Z", + "iopub.status.idle": "2023-09-06T21:39:55.095624Z", + "shell.execute_reply": "2023-09-06T21:39:55.095436Z" }, "papermill": { - "duration": 0.160508, - "end_time": "2022-01-21T05:23:06.688453", + "duration": 0.029093, + "end_time": "2023-09-06T21:39:55.096223", "exception": false, - "start_time": "2022-01-21T05:23:06.527945", + "start_time": "2023-09-06T21:39:55.067130", "status": "completed" }, "tags": [] @@ -4938,7 +4938,7 @@ " 5000.000000\n", " 5000.000000\n", " 5000.000000\n", - " 5000.000000\n", + " 5000.00000\n", " 5000.000000\n", " \n", " \n", @@ -4950,7 +4950,7 @@ " 2500.500000\n", " 2500.500000\n", " 2500.500000\n", - " 2500.500000\n", + " 2500.50000\n", " 2500.500000\n", " \n", " \n", @@ -4962,7 +4962,7 @@ " 1443.520003\n", " 1443.520003\n", " 1443.520003\n", - " 1441.676821\n", + " 1441.76128\n", " 1443.520003\n", " \n", " \n", @@ -4974,7 +4974,7 @@ " 1.000000\n", " 1.000000\n", " 1.000000\n", - " 1.000000\n", + " 1.00000\n", " 1.000000\n", " \n", " \n", @@ -4986,7 +4986,7 @@ " 1250.750000\n", " 1250.750000\n", " 1250.750000\n", - " 1250.750000\n", + " 1250.75000\n", " 1250.750000\n", " \n", " \n", @@ -4998,7 +4998,7 @@ " 2500.500000\n", " 2500.500000\n", " 2500.500000\n", - " 2500.500000\n", + " 2500.50000\n", " 2500.500000\n", " \n", " \n", @@ -5010,7 +5010,7 @@ " 3750.250000\n", " 3750.250000\n", " 3750.250000\n", - " 3619.000000\n", + " 3626.50000\n", " 3750.250000\n", " \n", " \n", @@ -5022,7 +5022,7 @@ " 5000.000000\n", " 5000.000000\n", " 5000.000000\n", - " 5000.000000\n", + " 5000.00000\n", " 5000.000000\n", " \n", " \n", @@ -5040,15 +5040,15 @@ "75% 3750.250000 3641.500000 3750.250000 3750.250000 3750.250000 \n", "max 5000.000000 5000.000000 5000.000000 5000.000000 5000.000000 \n", "\n", - " mad_log2 var_pc_log2 cv_pc_log2 mad_pc_log2 \n", - "count 5000.000000 5000.000000 5000.000000 5000.000000 \n", - "mean 2500.500000 2500.500000 2500.500000 2500.500000 \n", - "std 1443.520003 1443.520003 1441.676821 1443.520003 \n", - "min 1.000000 1.000000 1.000000 1.000000 \n", - "25% 1250.750000 1250.750000 1250.750000 1250.750000 \n", - "50% 2500.500000 2500.500000 2500.500000 2500.500000 \n", - "75% 3750.250000 3750.250000 3619.000000 3750.250000 \n", - "max 5000.000000 5000.000000 5000.000000 5000.000000 " + " mad_log2 var_pc_log2 cv_pc_log2 mad_pc_log2 \n", + "count 5000.000000 5000.000000 5000.00000 5000.000000 \n", + "mean 2500.500000 2500.500000 2500.50000 2500.500000 \n", + "std 1443.520003 1443.520003 1441.76128 1443.520003 \n", + "min 1.000000 1.000000 1.00000 1.000000 \n", + "25% 1250.750000 1250.750000 1250.75000 1250.750000 \n", + "50% 2500.500000 2500.500000 2500.50000 2500.500000 \n", + "75% 3750.250000 3750.250000 3626.50000 3750.250000 \n", + "max 5000.000000 5000.000000 5000.00000 5000.000000 " ] }, "metadata": {}, @@ -5069,16 +5069,16 @@ "id": "66a1a21f-5a0d-4965-b5bd-d006dff3525d", "metadata": { "execution": { - 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" 0.01741\n", - " 0.000\n", + " 0.03757\n", + " 0.0000\n", + " 0.01742\n", " 0.00000\n", + " 0.02762\n", + " 0.04834\n", " 0.00000\n", - " 0.01921\n", - " 0.000\n", " 0.000\n", + " 0.0000\n", " 0.00000\n", - " 0.00000\n", - " 0.000\n", " ...\n", - " 0.02747\n", - " 0.000\n", + " 0.0000\n", " 0.00000\n", - " 0.02358\n", - " 0.01574\n", + " 0.0473\n", " 0.00000\n", + " 0.0000\n", " 0.000\n", - " 0.000\n", - " 0.000\n", - " 0.02943\n", + " 0.07783\n", + " 0.00000\n", + " 0.00000\n", + " 0.03629\n", " \n", " \n", " ENSG00000227232.5\n", - " 3.08300\n", - " 7.071\n", - " 2.60300\n", - " 8.50100\n", - " 1.02600\n", - " 3.699\n", - " 2.418\n", - " 5.45200\n", - " 5.16400\n", - " 6.111\n", + " 0.92950\n", + " 1.3960\n", + " 1.52000\n", + " 1.56500\n", + " 1.54600\n", + " 5.75800\n", + " 3.87800\n", + " 1.553\n", + " 6.8610\n", + " 1.84000\n", " ...\n", - " 5.90100\n", - " 7.256\n", - " 12.58000\n", - " 7.55400\n", - " 3.09500\n", - " 5.93000\n", - " 5.136\n", - " 5.515\n", - " 3.736\n", - " 4.02300\n", + " 1.4070\n", + " 1.12700\n", + " 3.2030\n", + " 2.63600\n", + " 2.5360\n", + " 1.168\n", + " 5.77600\n", + " 1.91600\n", + " 5.96800\n", + " 2.26800\n", " \n", " \n", " ENSG00000278267.1\n", " 0.00000\n", - " 0.000\n", + " 0.0000\n", " 0.00000\n", " 0.00000\n", " 0.00000\n", - " 0.000\n", - " 0.000\n", " 0.00000\n", " 0.00000\n", " 0.000\n", + " 0.0000\n", + " 0.00000\n", " ...\n", + " 0.0000\n", " 0.00000\n", + " 0.0000\n", + " 0.39600\n", + " 0.0000\n", " 0.000\n", " 0.00000\n", " 0.00000\n", " 0.00000\n", " 0.00000\n", - " 0.000\n", - " 0.000\n", - " 0.000\n", - " 0.00000\n", " \n", " \n", " ENSG00000243485.5\n", - " 0.03476\n", - " 0.000\n", - " 0.03440\n", - " 0.04011\n", - " 0.03836\n", - " 0.000\n", - " 0.000\n", - " 0.04644\n", - " 0.00000\n", - " 0.000\n", - " ...\n", " 0.00000\n", - " 0.000\n", - " 0.07844\n", + " 0.0793\n", " 0.00000\n", " 0.00000\n", " 0.00000\n", + " 0.04825\n", + " 0.09592\n", " 0.000\n", - " 0.000\n", + " 0.0384\n", + " 0.00000\n", + " ...\n", + " 0.0415\n", + " 0.03456\n", + " 0.0000\n", + " 0.06219\n", + " 0.0405\n", " 0.000\n", " 0.00000\n", + " 0.06296\n", + " 0.02164\n", + " 0.00000\n", " \n", " \n", " ENSG00000237613.2\n", " 0.00000\n", - " 0.000\n", - " 0.04888\n", - " 0.02850\n", - " 0.00000\n", - " 0.000\n", - " 0.000\n", + " 0.0000\n", " 0.00000\n", - " 0.04808\n", + " 0.04263\n", + " 0.07835\n", + " 0.03428\n", + " 0.03407\n", " 0.000\n", + " 0.0000\n", + " 0.05345\n", " ...\n", + " 0.0000\n", " 0.00000\n", + " 0.0000\n", + " 0.02209\n", + " 0.0000\n", " 0.000\n", + " 0.03680\n", + " 0.01491\n", " 0.00000\n", " 0.00000\n", - " 0.00000\n", - " 0.03106\n", - " 0.000\n", - " 0.000\n", - " 0.000\n", - " 0.00000\n", " \n", " \n", "\n", - "

5 rows × 21 columns

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5 rows × 258 columns

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" GTEX-RU72-2526-SM-EWRML GTEX-S32W-1126-SM-4AD5V \\\n", - "gene_ens_id \n", - "ENSG00000223972.5 0.01921 0.000 \n", - "ENSG00000227232.5 1.02600 3.699 \n", - "ENSG00000278267.1 0.00000 0.000 \n", - "ENSG00000243485.5 0.03836 0.000 \n", - "ENSG00000237613.2 0.00000 0.000 \n", + " GTEX-11DXX-0126-SM-5EGH7 GTEX-11DXY-1626-SM-5H12L \\\n", + "gene_ens_id \n", + "ENSG00000223972.5 0.02762 0.04834 \n", + "ENSG00000227232.5 1.54600 5.75800 \n", + "ENSG00000278267.1 0.00000 0.00000 \n", + "ENSG00000243485.5 0.00000 0.04825 \n", + "ENSG00000237613.2 0.07835 0.03428 \n", "\n", - " GTEX-S33H-1926-SM-EYYVH GTEX-S3XE-1226-SM-4AD4L \\\n", - "gene_ens_id \n", - "ENSG00000223972.5 0.000 0.00000 \n", - "ENSG00000227232.5 2.418 5.45200 \n", - "ENSG00000278267.1 0.000 0.00000 \n", - "ENSG00000243485.5 0.000 0.04644 \n", - "ENSG00000237613.2 0.000 0.00000 \n", + " GTEX-11DXZ-0226-SM-5EGGZ GTEX-11EM3-0326-SM-5A5KJ \\\n", + "gene_ens_id \n", + "ENSG00000223972.5 0.00000 0.000 \n", + "ENSG00000227232.5 3.87800 1.553 \n", + "ENSG00000278267.1 0.00000 0.000 \n", + "ENSG00000243485.5 0.09592 0.000 \n", + "ENSG00000237613.2 0.03407 0.000 \n", "\n", - " GTEX-S4Q7-0926-SM-4AD5D GTEX-S4UY-0926-SM-4AD6O ... \\\n", - "gene_ens_id ... \n", - "ENSG00000223972.5 0.00000 0.000 ... \n", - "ENSG00000227232.5 5.16400 6.111 ... \n", - "ENSG00000278267.1 0.00000 0.000 ... \n", - "ENSG00000243485.5 0.00000 0.000 ... \n", - "ENSG00000237613.2 0.04808 0.000 ... \n", + " GTEX-11EMC-0526-SM-5EGJN GTEX-11EQ9-0126-SM-5986I ... \\\n", + "gene_ens_id ... \n", + "ENSG00000223972.5 0.0000 0.00000 ... \n", + "ENSG00000227232.5 6.8610 1.84000 ... \n", + "ENSG00000278267.1 0.0000 0.00000 ... \n", + "ENSG00000243485.5 0.0384 0.00000 ... \n", + "ENSG00000237613.2 0.0000 0.05345 ... \n", "\n", - " GTEX-SE5C-1026-SM-4BRUG GTEX-SNMC-0826-SM-4DM66 \\\n", + " GTEX-ZT9W-0126-SM-4YCFD GTEX-ZT9X-0126-SM-4YCFC \\\n", "gene_ens_id \n", - "ENSG00000223972.5 0.02747 0.000 \n", - "ENSG00000227232.5 5.90100 7.256 \n", - "ENSG00000278267.1 0.00000 0.000 \n", - "ENSG00000243485.5 0.00000 0.000 \n", - "ENSG00000237613.2 0.00000 0.000 \n", + "ENSG00000223972.5 0.0000 0.00000 \n", + "ENSG00000227232.5 1.4070 1.12700 \n", + "ENSG00000278267.1 0.0000 0.00000 \n", + "ENSG00000243485.5 0.0415 0.03456 \n", + "ENSG00000237613.2 0.0000 0.00000 \n", "\n", - " GTEX-SNOS-0526-SM-4DM54 GTEX-T2YK-2326-SM-EZ6LA \\\n", + " GTEX-ZTSS-0326-SM-5987M GTEX-ZUA1-1926-SM-5E45E \\\n", "gene_ens_id \n", - "ENSG00000223972.5 0.00000 0.02358 \n", - "ENSG00000227232.5 12.58000 7.55400 \n", - "ENSG00000278267.1 0.00000 0.00000 \n", - "ENSG00000243485.5 0.07844 0.00000 \n", - "ENSG00000237613.2 0.00000 0.00000 \n", + "ENSG00000223972.5 0.0473 0.00000 \n", + "ENSG00000227232.5 3.2030 2.63600 \n", + "ENSG00000278267.1 0.0000 0.39600 \n", + "ENSG00000243485.5 0.0000 0.06219 \n", + "ENSG00000237613.2 0.0000 0.02209 \n", "\n", - " GTEX-T5JW-1026-SM-EZ6LR GTEX-T6MN-2226-SM-EVYAM \\\n", + " GTEX-ZVP2-0126-SM-5NQ7D GTEX-ZVT2-0826-SM-5GIEO \\\n", "gene_ens_id \n", - "ENSG00000223972.5 0.01574 0.00000 \n", - "ENSG00000227232.5 3.09500 5.93000 \n", - "ENSG00000278267.1 0.00000 0.00000 \n", - "ENSG00000243485.5 0.00000 0.00000 \n", - "ENSG00000237613.2 0.00000 0.03106 \n", + "ENSG00000223972.5 0.0000 0.000 \n", + "ENSG00000227232.5 2.5360 1.168 \n", + "ENSG00000278267.1 0.0000 0.000 \n", + "ENSG00000243485.5 0.0405 0.000 \n", + "ENSG00000237613.2 0.0000 0.000 \n", "\n", - " GTEX-TMMY-1526-SM-4DXST GTEX-U3ZM-0826-SM-4DXU6 \\\n", + " GTEX-ZY6K-0126-SM-5SIAM GTEX-ZYFG-0926-SM-5BC5U \\\n", "gene_ens_id \n", - "ENSG00000223972.5 0.000 0.000 \n", - "ENSG00000227232.5 5.136 5.515 \n", - "ENSG00000278267.1 0.000 0.000 \n", - "ENSG00000243485.5 0.000 0.000 \n", - "ENSG00000237613.2 0.000 0.000 \n", + "ENSG00000223972.5 0.07783 0.00000 \n", + "ENSG00000227232.5 5.77600 1.91600 \n", + "ENSG00000278267.1 0.00000 0.00000 \n", + "ENSG00000243485.5 0.00000 0.06296 \n", + "ENSG00000237613.2 0.03680 0.01491 \n", "\n", - " GTEX-U3ZN-1226-SM-4DXUD GTEX-U4B1-1226-SM-4DXT7 \n", + " GTEX-ZYVF-1626-SM-5N9EH GTEX-ZZPU-1226-SM-5N9CK \n", "gene_ens_id \n", - "ENSG00000223972.5 0.000 0.02943 \n", - "ENSG00000227232.5 3.736 4.02300 \n", - "ENSG00000278267.1 0.000 0.00000 \n", - "ENSG00000243485.5 0.000 0.00000 \n", - "ENSG00000237613.2 0.000 0.00000 \n", + "ENSG00000223972.5 0.00000 0.03629 \n", + "ENSG00000227232.5 5.96800 2.26800 \n", + "ENSG00000278267.1 0.00000 0.00000 \n", + "ENSG00000243485.5 0.02164 0.00000 \n", + "ENSG00000237613.2 0.00000 0.00000 \n", "\n", - "[5 rows x 21 columns]" + "[5 rows x 258 columns]" ] }, "execution_count": 12, @@ -1111,10 +1111,10 @@ "id": "dd851f15-ad05-4eda-9af8-2cd8d383a45b", "metadata": { "papermill": { - "duration": 0.027857, - "end_time": "2022-01-24T20:12:37.464906", + "duration": 0.002302, + "end_time": "2023-09-06T21:40:27.677380", "exception": false, - "start_time": "2022-01-24T20:12:37.437049", + "start_time": "2023-09-06T21:40:27.675078", "status": "completed" }, "tags": [] @@ -1125,20 +1125,20 @@ }, { "cell_type": "code", - "execution_count": 16, + "execution_count": 13, "id": "06c8e283-64d6-4be7-8fd3-0de9a1f1d8b0", "metadata": { "execution": { - "iopub.execute_input": "2022-01-24T20:12:37.525127Z", - "iopub.status.busy": "2022-01-24T20:12:37.524562Z", - "iopub.status.idle": "2022-01-24T20:12:37.527403Z", - "shell.execute_reply": "2022-01-24T20:12:37.527024Z" + "iopub.execute_input": "2023-09-06T21:40:27.682340Z", + "iopub.status.busy": "2023-09-06T21:40:27.682227Z", + "iopub.status.idle": "2023-09-06T21:40:27.684019Z", + "shell.execute_reply": "2023-09-06T21:40:27.683886Z" }, "papermill": { - 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"start_time": "2022-01-24T20:12:39.116658", + "start_time": "2023-09-06T21:40:27.872795", "status": "completed" }, "tags": [] @@ -2379,10 +2379,10 @@ "id": "588803c0-0655-4af7-8721-ca8ceba871cf", "metadata": { "papermill": { - "duration": 0.033499, - "end_time": "2022-01-24T20:12:39.247828", + "duration": 0.00271, + "end_time": "2023-09-06T21:40:27.893674", "exception": false, - "start_time": "2022-01-24T20:12:39.214329", + "start_time": "2023-09-06T21:40:27.890964", "status": "completed" }, "tags": [] @@ -2410,18 +2410,18 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.9" + "version": "3.9.12" }, "papermill": { "default_parameters": {}, - "duration": 5.169549, - "end_time": "2022-01-24T20:12:39.489386", + "duration": 1.511249, + "end_time": "2023-09-06T21:40:28.011752", "environment_variables": {}, "exception": null, "input_path": "nbs/05_preprocessing/07-gtex_v8-metadata.ipynb", "output_path": "nbs/05_preprocessing/07-gtex_v8-metadata.run.ipynb", "parameters": {}, - "start_time": "2022-01-24T20:12:34.319837", + "start_time": "2023-09-06T21:40:26.500503", "version": "2.3.3" } }, diff --git a/nbs/05_preprocessing/py/00-gtex_v8-split_by_tissue.py b/nbs/05_preprocessing/py/00-gtex_v8-split_by_tissue.py index 1a766bb4..0142dda6 100644 --- a/nbs/05_preprocessing/py/00-gtex_v8-split_by_tissue.py +++ b/nbs/05_preprocessing/py/00-gtex_v8-split_by_tissue.py @@ -2,11 +2,11 @@ # jupyter: # jupytext: # cell_metadata_filter: all,-execution,-papermill,-trusted +# notebook_metadata_filter: -jupytext.text_representation.jupytext_version # text_representation: # extension: .py # format_name: percent # format_version: '1.3' -# jupytext_version: 1.11.5 # kernelspec: # display_name: Python 3 (ipykernel) # language: python diff --git a/nbs/05_preprocessing/py/05-gtex_v8-select_top_genes.py b/nbs/05_preprocessing/py/05-gtex_v8-select_top_genes.py index 4d569454..da2a40f4 100644 --- a/nbs/05_preprocessing/py/05-gtex_v8-select_top_genes.py +++ b/nbs/05_preprocessing/py/05-gtex_v8-select_top_genes.py @@ -2,11 +2,11 @@ # jupyter: # jupytext: # cell_metadata_filter: all,-execution,-papermill,-trusted +# notebook_metadata_filter: -jupytext.text_representation.jupytext_version # text_representation: # extension: .py # format_name: percent # format_version: '1.3' -# jupytext_version: 1.11.5 # kernelspec: # display_name: Python 3 (ipykernel) # language: python diff --git a/nbs/05_preprocessing/py/07-gtex_v8-metadata.py b/nbs/05_preprocessing/py/07-gtex_v8-metadata.py index b972c5ee..f176f792 100644 --- a/nbs/05_preprocessing/py/07-gtex_v8-metadata.py +++ b/nbs/05_preprocessing/py/07-gtex_v8-metadata.py @@ -2,11 +2,11 @@ # jupyter: # jupytext: # cell_metadata_filter: all,-execution,-papermill,-trusted +# notebook_metadata_filter: -jupytext.text_representation.jupytext_version # text_representation: # extension: .py # format_name: percent # format_version: '1.3' -# jupytext_version: 1.11.5 # kernelspec: # display_name: Python 3 (ipykernel) # language: python