Pluto Quick-Start for Academia

    • Rani Powers |
    • 0 step |
    • 2 minutes

      Welcome to Pluto

      To get started, check your inbox for the invitation email. Click the "Accept Invitation" button in the email and sign up for a new account, or log in if you've already created one.
      Once logged in, navigate to your Lab Space (https://pluto.bio/labspace). You Lab Space may look a little empty when you're just starting out, but soon it will be full of projects and experiments!

      Creating a project

      In Pluto, a project is a collection of experiments. Projects are the colored tiles in your Lab Space and show user icons for anyone who has access to the project. Projects can be personal (private to you until you share them), or team projects (indicated by a team icon and name such as "Molecular Oncology Group" below).
      Click "+ Project" to create a new project
      Give your project an informative name, such as the title of a manuscript or statement of a scientific hypothesis
      Select "Personal" for the project type if the project will be private to only you and certain collaborators. For easier collaboration, you can also choose the "Team" project type.
      When creating a team project, select the team you'd like to be able to view all experiments in the project. Alternatively, select your organization name ("Powers Lab at Pluto University" in the example below) to let everyone in your organization view the experiments.
      Click "Save & Close"
      You're now ready to begin adding experiments to your newly created project!

      Creating an experiment

      You can analyze a variety of assays or experiment types in Pluto, including RNA-seq, ChIP-seq, CUT&RUN, and lower-throughput assays like qPCR and ELISAs. The experiment types you'll see in your Lab Space are based on your team's subscription.
      Not seeing an experiment type you need? Reach out to your Pluto rep any time to discuss upgrading to another plan
      From your Lab Space, click "+ Experiment" to create a new experiment
      Select the project the experiment should live under, and give the experiment an informative name
      Tip! Pluto experiment tiles display the organism and experiment type by default so there's no need to include things like "human" or "RNA-seq" in the experiment's name
      Select the organism and type of experiment
      Click "Continue" to move on to the assay data upload step
      For sequencing-based experiments, you'll see multiple options for uploading assay data. You can drag and drop in FASTQ files on the first tab
      Or click on the "CSV" tab to upload an already-processed count matrix. If the data is in a public repository or cloud-based location, select the "Other" tab for instructions on how to upload it.
      After uploading your assay data, click Continue in the bottom right corner. You can also click "Annotate your samples" to move directly to the sample annotation step.
      Using one of the available templates, create a sample annotation table for your experiment and drop the completed template into the dashed line region, then click "Continue".
      If you uploaded FASTQ files, you'll be prompted to configure your desired pipeline parameters in the final step. Click "Run pipeline" to begin processing your FASTQ files!

      Analyzing an experiment

      Click into an experiment to begin your analysis. Use the blue "+ Analysis" button to open up the analysis sidebar and select an analysis.
      In the sidebar, select an analysis you'd like to run
      Click "Next"
      Once created, you can customize your plots by clicking the "..." in the upper right of any plot > "Edit" > make your changes and click "View Changes" in the lower left.
      Continue adding more new analyses to your experiment using the "+ Analysis" button. Happy exploring!
      Pluto supports a wide variety of analysis types, and the plots you'll create are highly customizable. Check out our help docs at [https://help.pluto.bio](https://help.pluto.bio) for how-to guides and inspiration!

      Inviting collaborators

      Invite collaborators to your organization from the Team tab
      You can also invite collaborators to an individual project or experiment by clicking the "..." > Invite
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