├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ └── feature_request.md ├── PULL_REQUEST_TEMPLATE.md └── workflows │ ├── check-links.yaml │ └── notebook-lint.yaml ├── AWS ├── 01-RNA-Seq │ ├── RNA-seq.ipynb │ ├── install_rna_seq_packages.sh │ └── rnaseq-aws.config ├── 02-RRBS │ ├── RRBS-downstream.ipynb │ ├── install_rrbs_packages.sh │ └── rrbs-aws.config ├── 03-Integration │ ├── Integration.ipynb │ └── install_integration_packages.sh ├── 04-Bonus-New-Data │ └── 04_New_Data.ipynb └── README.md ├── GoogleCloud ├── 01-RNA-Seq │ ├── RNA-seq.ipynb │ ├── install_rna_seq_packages.sh │ ├── rnaseq-gcb.config │ └── util │ │ └── gemini.py ├── 02-RRBS │ ├── RRBS-downstream.ipynb │ ├── install_rrbs_packages.sh │ └── rrbs-gcb.config ├── 03-Integration │ ├── Integration.ipynb │ └── install_integration_packages.sh ├── 04-Bonus-New-Data │ └── 04_New_Data.ipynb └── README.md ├── ISSUE_TEMPLATE ├── bug_report.md └── feature_request.md ├── PULL_REQUEST_TEMPLATE.md ├── README.md ├── images ├── Advanced_options.png ├── Create-R-notebook.png ├── Create_new_notebook.png ├── Customize-notebook.png ├── DNAMethylation.png ├── Initial-screen-after-clone.png ├── LaunchStack.jpg ├── RNA-Seq_Notebook_Homepage.png ├── UND-course-card-2.png ├── User-Notebook-creation.png ├── architecture-aws.png ├── architecture-gcp.png ├── central-dogma.jpeg ├── enable_auto_shutdown_mins.png ├── enable_idle_shutdown_mins.png ├── epigenetic-mech.jpeg ├── integration.png ├── methylation-celltype.png ├── methylation-experiment.png ├── methylation-flowchart.jpeg ├── methylation-hclust.png ├── methylation-pvclust.png ├── methylation-towards.jpeg ├── nfcore-methylseq.png ├── nfcore-rnaseq.png ├── ngs.png ├── read_counts.png └── rna-seq-roadmap.png └── quiz_files ├── methylation.html ├── methylation.ipynb ├── methylation.json ├── rna-pre_module.html ├── rna-pre_module.ipynb └── rna-pre_module.json /.github/ISSUE_TEMPLATE/bug_report.md: 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