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Clarifying quickstart
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ashleymaeconard authored Nov 20, 2023
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Expand Up @@ -28,9 +28,11 @@ Multioviz is a free, user-friendly, interactive platform that facilitates *in si
## Quickstart: 3 usages
Multioviz has three usages: To (1) visualize ranked molecular features as GRNs and (2) perturb GRNs for *in silico* hypothesis testing, click [here](https://multioviz-de57keuawa-uc.a.run.app/). The user can also (3) integrate their own computational method that performs feature selection and perturbation through the multioviz R package (see installation steps [here](#installation)).

1. For (1), under the "Visualize" drop down (side bar), upload the [required inputs](#a-visualize), set network preferences, and click "RUN" to visualize the user's data. See the [visualization instructions](#a-visualize-ranked-molecular-features-as-a-grn) for a detailed walk through.
2. For (2), under the "Perturb" drown down (side bar), upload the [required inputs](#b-perturb), and click "RUN" to generate the network. For a detailed walk through on how to perturb and rerun the user's network, visit the [perturbation](#b-generate-a-perturbable-grn-to-test-hypotheses-in-silico) section.
3. For (3), once the multioviz package is installed, open a new R session (```R```) and load the package (```library multioviz```). Run ```runMultioviz()``` with no arguments to generate a demo network, and with the [required arguments](#c-integrate-computational-method) to generate a network using the user's own method. Visit the [method integration](#c-integrate-feature-selection-and-prioritization-method) section for more detailed instructions.
1. For (1), to quickly visualize a GRN, press "Load Demo Files" and press "RUN" to see the GRN!
- To load your own data, under the "Visualize" drop down (side bar), upload the [required inputs](#a-visualize), set network preferences, and click "RUN" to visualize the user's data. See the [visualization instructions](#a-visualize-ranked-molecular-features-as-a-grn) for a detailed walk-through.
3. For (2), to quickly perturb a GRN, press "Load Demo Files" and press "RUN" to see the GRN, followed by clicking any node, then clicking "Edit" to "Delete" or "Edit" the node. Then click "RERUN".
- To load your own data, under the "Perturb" drown down (side bar), upload the [required inputs](#b-perturb), and click "RUN" to generate the network. For a detailed walk through on how to perturb and rerun the user's network, visit the [perturbation](#b-generate-a-perturbable-grn-to-test-hypotheses-in-silico) section.
5. For (3), once the multioviz package is installed, open a new R session (```R```) and load the package (```library multioviz```). Run ```runMultioviz()``` with no arguments to generate a demo network, and with the [required arguments](#c-integrate-computational-method) to generate a network using the user's own method. Visit the [method integration](#c-integrate-feature-selection-and-prioritization-method) section for more detailed instructions.

## Dependencies
- R (>= 4.1.2)
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