Skip to content

Commit 6466261

Browse files
author
github-action
committed
Github Action: Lint Notebooks
1 parent 1b81e21 commit 6466261

File tree

2 files changed

+58
-290
lines changed

2 files changed

+58
-290
lines changed

‎AWS/01-RNA-Seq/RNA-seq.ipynb

Lines changed: 21 additions & 105 deletions
Original file line numberDiff line numberDiff line change
@@ -20,11 +20,7 @@
2020
"cell_type": "code",
2121
"execution_count": null,
2222
"id": "1c2d28e0",
23-
"metadata": {
24-
"vscode": {
25-
"languageId": "r"
26-
}
27-
},
23+
"metadata": {},
2824
"outputs": [],
2925
"source": [
3026
"IRdisplay::display_html('<iframe src = \"../../quiz_files/rna-pre_module.html\" width=95% height=600></iframe>')"
@@ -205,11 +201,7 @@
205201
"cell_type": "code",
206202
"execution_count": null,
207203
"id": "95cda0d2",
208-
"metadata": {
209-
"vscode": {
210-
"languageId": "r"
211-
}
212-
},
204+
"metadata": {},
213205
"outputs": [],
214206
"source": [
215207
"system('chmod +x install_rna_seq_packages.sh' , intern=TRUE)\n",
@@ -253,11 +245,7 @@
253245
"cell_type": "code",
254246
"execution_count": null,
255247
"id": "6da16610-a83f-42b5-be52-f8116db3fb03",
256-
"metadata": {
257-
"vscode": {
258-
"languageId": "r"
259-
}
260-
},
248+
"metadata": {},
261249
"outputs": [],
262250
"source": [
263251
"#Install nexflow, make it exceutable, and update it\n",
@@ -292,11 +280,7 @@
292280
"cell_type": "code",
293281
"execution_count": null,
294282
"id": "bb2e1f61-eea1-4464-9842-76fabae4c39a",
295-
"metadata": {
296-
"vscode": {
297-
"languageId": "r"
298-
}
299-
},
283+
"metadata": {},
300284
"outputs": [],
301285
"source": [
302286
"system('./nextflow run nf-core/rnaseq -c rnaseq-aws.config -profile test,aws', intern=TRUE)"
@@ -333,11 +317,7 @@
333317
"cell_type": "code",
334318
"execution_count": null,
335319
"id": "a5ea70df-98ba-4a69-aeec-2baed34a72fc",
336-
"metadata": {
337-
"vscode": {
338-
"languageId": "r"
339-
}
340-
},
320+
"metadata": {},
341321
"outputs": [],
342322
"source": [
343323
"library(DESeq2)\n",
@@ -360,11 +340,7 @@
360340
"cell_type": "code",
361341
"execution_count": null,
362342
"id": "e49c7007-61b3-4057-89de-3f3fb1085800",
363-
"metadata": {
364-
"vscode": {
365-
"languageId": "r"
366-
}
367-
},
343+
"metadata": {},
368344
"outputs": [],
369345
"source": [
370346
"# download data files from storage bucket\n",
@@ -399,11 +375,7 @@
399375
"cell_type": "code",
400376
"execution_count": null,
401377
"id": "5fce0d5b-740b-4f9c-8479-fa60a0566532",
402-
"metadata": {
403-
"vscode": {
404-
"languageId": "r"
405-
}
406-
},
378+
"metadata": {},
407379
"outputs": [],
408380
"source": [
409381
"DESeq.ds <- DESeqDataSetFromMatrix(countData = round(readcounts), colData = sample_info, design = ~condition)\n"
@@ -423,11 +395,7 @@
423395
"cell_type": "code",
424396
"execution_count": null,
425397
"id": "cb7c8095-8d5c-4165-a0bf-9acfec7d97fe",
426-
"metadata": {
427-
"vscode": {
428-
"languageId": "r"
429-
}
430-
},
398+
"metadata": {},
431399
"outputs": [],
432400
"source": [
433401
"colData(DESeq.ds) %>% head\n",
@@ -452,11 +420,7 @@
452420
"cell_type": "code",
453421
"execution_count": null,
454422
"id": "4fc2ab39-8608-435b-a8f9-fb6f379be65a",
455-
"metadata": {
456-
"vscode": {
457-
"languageId": "r"
458-
}
459-
},
423+
"metadata": {},
460424
"outputs": [],
461425
"source": [
462426
"DESeq.ds <- DESeq.ds[ rowSums(counts(DESeq.ds)) > 0, ]\n",
@@ -480,11 +444,7 @@
480444
"cell_type": "code",
481445
"execution_count": null,
482446
"id": "40aa5366-4c12-4443-99a9-39ac707639d3",
483-
"metadata": {
484-
"vscode": {
485-
"languageId": "r"
486-
}
487-
},
447+
"metadata": {},
488448
"outputs": [],
489449
"source": [
490450
"# Get the size factor using estimateSizeFactors from DESeq.\n",
@@ -509,11 +469,7 @@
509469
"cell_type": "code",
510470
"execution_count": null,
511471
"id": "38523c0a-b9af-49ca-b7e8-2dbb4604fe5c",
512-
"metadata": {
513-
"vscode": {
514-
"languageId": "r"
515-
}
516-
},
472+
"metadata": {},
517473
"outputs": [],
518474
"source": [
519475
"# transform size-factor normalized read counts to log2 scale using pseudocount of 1\n",
@@ -542,11 +498,7 @@
542498
"cell_type": "code",
543499
"execution_count": null,
544500
"id": "a283f6d7-3370-41e7-a85c-c54c695f721f",
545-
"metadata": {
546-
"vscode": {
547-
"languageId": "r"
548-
}
549-
},
501+
"metadata": {},
550502
"outputs": [],
551503
"source": [
552504
"# mean-sd plot\n",
@@ -574,11 +526,7 @@
574526
"cell_type": "code",
575527
"execution_count": null,
576528
"id": "8f444ca6-b525-4e2e-9f9e-4363663b45fc",
577-
"metadata": {
578-
"vscode": {
579-
"languageId": "r"
580-
}
581-
},
529+
"metadata": {},
582530
"outputs": [],
583531
"source": [
584532
"# Regularized log-transformed values\n",
@@ -606,11 +554,7 @@
606554
"cell_type": "code",
607555
"execution_count": null,
608556
"id": "8ca292e8-27a2-4336-b047-07751cef499d",
609-
"metadata": {
610-
"vscode": {
611-
"languageId": "r"
612-
}
613-
},
557+
"metadata": {},
614558
"outputs": [],
615559
"source": [
616560
"# cor() calculates the correlation between columns of a matrix\n",
@@ -638,11 +582,7 @@
638582
"cell_type": "code",
639583
"execution_count": null,
640584
"id": "b38f5fab-4b48-4e74-9e23-793e202312dc",
641-
"metadata": {
642-
"vscode": {
643-
"languageId": "r"
644-
}
645-
},
585+
"metadata": {},
646586
"outputs": [],
647587
"source": [
648588
"P <- plotPCA(DESeq.rlog)\n",
@@ -665,11 +605,7 @@
665605
"cell_type": "code",
666606
"execution_count": null,
667607
"id": "f36513db-22f6-417f-aaa8-39ba1837ca35",
668-
"metadata": {
669-
"vscode": {
670-
"languageId": "r"
671-
}
672-
},
608+
"metadata": {},
673609
"outputs": [],
674610
"source": [
675611
"# DESeq2 uses the levels of the condition to determine the order of the comparison\n",
@@ -692,11 +628,7 @@
692628
"cell_type": "code",
693629
"execution_count": null,
694630
"id": "17827bd4-0938-49e8-9f3a-b4e979fedb3a",
695-
"metadata": {
696-
"vscode": {
697-
"languageId": "r"
698-
}
699-
},
631+
"metadata": {},
700632
"outputs": [],
701633
"source": [
702634
"#Check the results of deseq analysis\n",
@@ -717,11 +649,7 @@
717649
"cell_type": "code",
718650
"execution_count": null,
719651
"id": "39a986b0-3ee2-436a-927b-37f539e7c627",
720-
"metadata": {
721-
"vscode": {
722-
"languageId": "r"
723-
}
724-
},
652+
"metadata": {},
725653
"outputs": [],
726654
"source": [
727655
"#Histogram\n",
@@ -743,11 +671,7 @@
743671
"cell_type": "code",
744672
"execution_count": null,
745673
"id": "079404d0-d179-4bdf-8a2a-63e135b68c45",
746-
"metadata": {
747-
"vscode": {
748-
"languageId": "r"
749-
}
750-
},
674+
"metadata": {},
751675
"outputs": [],
752676
"source": [
753677
"#MA plot\n",
@@ -771,11 +695,7 @@
771695
"cell_type": "code",
772696
"execution_count": null,
773697
"id": "5bdda266-08e2-47fd-bdd8-f06cd4dd7f0c",
774-
"metadata": {
775-
"vscode": {
776-
"languageId": "r"
777-
}
778-
},
698+
"metadata": {},
779699
"outputs": [],
780700
"source": [
781701
"#HEATMAP\n",
@@ -819,11 +739,7 @@
819739
"cell_type": "code",
820740
"execution_count": null,
821741
"id": "38f62bcf-3150-417e-bebb-787763db04aa",
822-
"metadata": {
823-
"vscode": {
824-
"languageId": "r"
825-
}
826-
},
742+
"metadata": {},
827743
"outputs": [],
828744
"source": [
829745
"write.table(DGE.results.sorted, file=\"rna-seq_dge-results.txt\", sep = \"\\t\")"

0 commit comments

Comments
 (0)