From 323a9d224d7269ff42e2a38fe4e9d06ac26e6002 Mon Sep 17 00:00:00 2001 From: Ashley Mae Conard Date: Mon, 20 Nov 2023 08:52:25 -0500 Subject: [PATCH] Update README.md Clarifying quickstart --- README.md | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 1e09a63..ffb4ba6 100644 --- a/README.md +++ b/README.md @@ -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)