Tool: BioVinci: user-friendly software to make plotting easy - PCA, 3D scatter plot, venn diagram, you name it.
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9 months ago
Jennifer Pham • 290
San Diego CA

We would like to introduce BioVinci, a tool for biological data visualization and analysis. The software is user friendly and code free. The idea is to make running statistics and plotting easy without losing power. BioVinci allows you to:

  • Run any statistical analyses
  • Drag and drop to customize plots
  • Quickly create publication-ready data visuals.

Available for Linux, Mac OS, and Windows. Download here: https://vinci.bioturing.com

Highlight features:

1. Flexible graphing and customization - Output format: SVG (scalable vector graphics), EPS, PS, PNG, PDF - Unique plot type: violin plot, dendrogram, heatmap, 3D scatter plot - Optimized for tables up to 50,000 rows x 100 columns

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2. Machine learning and statistics - Dimensionality reduction (PCA 3D plots and biplots, t-SNE, etc.) - Clustering functions (k-means clustering and hierarchical clustering) - Hypothesis testing and regression

View the PCA tutorial here: https://www.youtube.com/watch?v=6truZBwKEm8

3. Sharing and collaboration - BVC file: to archive worksets, or share with collaborators - Share interactive graphs via emails, social platforms, URL

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Entering edit mode
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An enhancement : a function to transform the input matrix.

ADD REPLYlink 15 months ago
Zhilong Jia
♦ 1.4k
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hi Zhilong, BioVinci can now transform the input matrix well for data with replications. Is it what you refer to?

ADD REPLYlink 12 months ago
Jennifer Pham
• 290
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Seems like a UI for R. Can it plot the 3D PCA and biplots?

ADD REPLYlink 13 months ago
anne.bros
• 40
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Yes we used some popular libraries in R to ensure the accuracy. We do offer 3D PCA, biplots, scree plots, plots of loadings, and more. I believe the easy and interactive PCA is one of our strongest points so far.

ADD REPLYlink 13 months ago
Jennifer Pham
• 290
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seems pretty, but what linux do you support?

ADD REPLYlink 12 months ago
nathanlee
• 10
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we support ubuntu 16.04 and 18.04 LTS

ADD REPLYlink 8 months ago
Jennifer Pham
• 290
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Is this a commercial product?

ADD REPLYlink 12 months ago
Alex Reynolds
28k
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Yes, it is. But I believe it will help you save a lot of time for PCA, t-SNE, and other advanced analyses.

ADD REPLYlink 12 months ago
Jennifer Pham
• 290
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It may well do so, but I think we have rules about posts about commercial products.

ADD REPLYlink 12 months ago
Alex Reynolds
28k
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hi Alex, could you suggest any reference for posts about commercial products so that I can do it right?

ADD REPLYlink 12 months ago
Jennifer Pham
• 290
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thanks, the 3d pca looks great.

ADD REPLYlink 12 months ago
anne.bros
• 40
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thanks for your answer!

ADD REPLYlink 11 months ago
anne.bros
• 40
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Tried it, yet still didn't figure out how to create a 3D PCA. The typical 3D scatter plot was not difficult to find, but where is the 3D PCA?

ADD REPLYlink 13 months ago
anne.bros
• 40
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You can click Plot, and drag the third PC into the Z field. To find the third PC, check out the box on the bottom left corner of the screen. Here's a short tutorial for your reference:

ADD REPLYlink 8 months ago
Jennifer Pham
• 290
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i mean the pca or tsne results

ADD REPLYlink 12 months ago
nathanlee
• 10
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why not use R? It's free and does anything you want.

ADD REPLYlink 12 months ago
Nancy Watson
• 0
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R is free and powerful -- would be great if you can code. The learning curve is quite steep to some people, so we hope BioVinci can help them out.

ADD REPLYlink 12 months ago
Jennifer Pham
• 290
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Sure. The learning curve is steep, but it's rewarding. However, i'll give Biovinci a try for the days when I have no mood to code.

ADD REPLYlink 12 months ago
Nancy Watson
• 0
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That violin plot looks awesome. Is there a way to apply log scale for the data?

ADD REPLYlink 10 months ago
Shannon Berman
• 0
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Yes @Shannon, you can apply log scale for the axes.

ADD REPLYlink 8 months ago
Jennifer Pham
• 290
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The biplot seems not quite right.

ADD REPLYlink 9 months ago
nathanlee
• 10
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@nathanlee: I got it. The origins of the inner axes should have overlapped on each other. Yet you can adjust this in BioVinci

ADD REPLYlink 8 months ago
Jennifer Pham
• 290
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12 months ago
Jennifer Pham • 290
San Diego CA

guys, here's a quick guide on t-SNE in BioVinci:

ADD COMMENTlink 12 months ago Jennifer Pham • 290
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can i export the table of results or just the plots?

ADD REPLYlink 12 months ago
nathanlee
• 10
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yes, sure. In tsv files

ADD REPLYlink 12 months ago
Jennifer Pham
• 290
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11 months ago
Jennifer Pham • 290
San Diego CA

BioTuring and BioVinci were featured on Genomeweb last week. Here's to take a look: https://www.genomeweb.com/informatics/bioturing-launches-browser-single-cell-bulk-rna-seq-data#.W7rU1WgzaUl

ADD COMMENTlink 11 months ago Jennifer Pham • 290

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