Cellular Genetics IT travel guide

• The group
  • Our story
  • Our remit
  • Our vision
• Jira Requests
  • Datsharing
  • Pipelines
  • JupyterHub
  • GPU Notebooks
  • OMERO image uploads
  • ArrayExpress uploads
  • Websites
• Jupyter Hub
  • How to get access
  • Internal JupyterHub
  • Resources
  • Quick Start Guide
  • Notebook templates
  • Installing packages
  • Kernels
  • Managing your data
  • Sharing notebooks
  • iRODS
  • Running containers
  • Troubleshooting
  • How to get help
• GPU Notebooks on the Cloud
  • Request a notebook
  • Accessing your instance
  • Installed software
  • Getting data to the cloud
  • Shutting down your instance
• Notebooks
  • SoupX
  • Scrublet
  • Seurat
  • Scanpy
  • Integration in R
  • Integration in Python
  • Monocle3
• Rclone
  • Installation
  • Add rclone to your FARM PATH
  • FARM module load
  • Configuration
  • Usage Examples
  • Miscellaneous
• Getting raw fastq files
  • Databases and manual file download
  • SRA formats and NCBI SRA tools
  • Automation: fetching many samples at once
  • Downloading single cell datasets from SRA
  • Using ArrayExpress or ENA
  • Brief summary
• Imaging
  • Introduction
  • OMERO
  • OMERO uploads
  • Stitching
  • Segmentation
  • Registration
• Data sharing
  • Globus
  • cram files
• Data submission
  • ArrayExpress
  • EGA/ENA
• Nextflow pipelines
  • Notes
• ML Warehouse
  • Show me information for all the samples in a study
  • Show me information for all the samples with a cost code
  • Show me run ID, lane number and tag index for a sample
• Single Cell Visualizations
  • cellxgene
  • AnnData
  • Examples
  • Demo
• IGViewer on Remote Environments
  • FARM
  • JupyterHub
• Contact us
  • Submit a ticket
  • Coffee standups
  • Chat

Note

The creation of this travel guide was inspired by Patrick Kua