CCBB’s Bioinformatic framework for Scripps Research community!

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CCBB is empowering you with tools for self-directed data analysis

Please follow the instructions and get access to our analysis pipelines:

Step1

Sign-up for the pipelines you like to use (just once per pipeline).
Email CCBB to find out if you have signed up already!

Step2

To access our pipelines on Garibaldi, please get your account on Garibaldi by emailing HPC (if you do not have one already).

Step3

Setting up Workflow, an interface to access CCBB pipelines on Garibaldi:
Please follow the instructions to setup workflow on your computer.
In case of any questions in setting up workflow please reach out to the workflow support team
Please note that workflow needs to be set-up only once.

CCBB Pipelines on Garibaldi

  • Bulk RNAseq analysis user guide
  • Differential Abundance analysis user guide (prerequisite: run Bulk RNAseq analysis)
  • 10x single cell gene expression (standard) analysis user guide
NOTE:

You will receive an email when pipeline is completed. Please follow the instructions provided in this email to delete a pipeline generated intermediate files/folders to free up the space.

Custom analysis

Consult CCBB for any downstream custom work including generating figures for publication, comprehensive functional analysis (with our licensed product Advaita’s iPathwayGuide), submitting data to public repositories etc.

Please consider

Reviewing our authorship guidelines and giving authorship to CCBB personnel contributing to your research work. Include the following in the Acknowledgements section of your manuscript and recognize specific CCBB personnel who helped in your project(s): “The authors acknowledge the bioinformatic support of the Center for Computational Biology and Bioinformatics (CCBB) at Scripps Research”.
Co-authorship and acknowledgments demonstrate the utilization of our Bioinformatics Core services and is an indication of its value to your research.

Feedback

Please provide feedback at least once per pipeline you have used. We use your feedback to improve services and identify opportunities for enhanced support.

DISCLAIMER

CCBB is providing pipelines on Garibaldi, the institute’s shared Linux cluster, on “as is” and “as available” terms, solely for the benefit of the scientific community at Scripps Research. CCBB reserves the right to continue/discontinue any of its pipelines on Garibaldi.