Tool: BioVinci: user-friendly software to make plotting easy - PCA, 3D scatter plot, venn diagram, you name it.
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gravatar for Jennifer Pham
8 months ago by
Jennifer Pham260
San Diego CA
Jennifer Pham260 wrote:

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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rna-seq tool pca venn diagram gene • 2.3k views
ADD COMMENTlink modified 4 weeks ago • written 8 months ago by Jennifer Pham260
2

An enhancement : a function to transform the input matrix.

ADD REPLYlink written 7 months ago by Zhilong Jia1.4k

hi Zhilong, BioVinci can now transform the input matrix well for data with replications. Is it what you refer to?

ADD REPLYlink written 4 months ago by Jennifer Pham260
2

Seems like a UI for R. Can it plot the 3D PCA and biplots?

ADD REPLYlink written 5 months ago by anne.bros40
1

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 written 5 months ago by Jennifer Pham260
1

seems pretty, but what linux do you support?

ADD REPLYlink written 4 months ago by nathanlee10

we support ubuntu 16.04 and 18.04 LTS

ADD REPLYlink written 25 days ago by Jennifer Pham260
1

Is this a commercial product?

ADD REPLYlink written 4 months ago by Alex Reynolds27k

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 written 4 months ago by Jennifer Pham260

It may well do so, but I think we have rules about posts about commercial products.

ADD REPLYlink written 4 months ago by Alex Reynolds27k

hi Alex, could you suggest any reference for posts about commercial products so that I can do it right?

ADD REPLYlink written 4 months ago by Jennifer Pham260
1

thanks, the 3d pca looks great.

ADD REPLYlink written 4 months ago by anne.bros40
1

thanks for your answer!

ADD REPLYlink written 3 months ago by anne.bros40

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 written 5 months ago by anne.bros40

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 written 25 days ago by Jennifer Pham260

i mean the pca or tsne results

ADD REPLYlink written 4 months ago by nathanlee10

why not use R? It's free and does anything you want.

ADD REPLYlink written 4 months ago by Nancy Watson0
1

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 written 4 months ago by Jennifer Pham260

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 written 4 months ago by Nancy Watson0

That violin plot looks awesome. Is there a way to apply log scale for the data?

ADD REPLYlink written 11 weeks ago by Shannon Berman0

Yes @Shannon, you can apply log scale for the axes.

ADD REPLYlink written 25 days ago by Jennifer Pham260

The biplot seems not quite right.

ADD REPLYlink written 7 weeks ago by nathanlee10

@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 written 25 days ago by Jennifer Pham260
1
gravatar for Jennifer Pham
4 months ago by
Jennifer Pham260
San Diego CA
Jennifer Pham260 wrote:

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

ADD COMMENTlink written 4 months ago by Jennifer Pham260

can i export the table of results or just the plots?

ADD REPLYlink written 4 months ago by nathanlee10

yes, sure. In tsv files

ADD REPLYlink written 4 months ago by Jennifer Pham260
0
gravatar for Jennifer Pham
3 months ago by
Jennifer Pham260
San Diego CA
Jennifer Pham260 wrote:

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 written 3 months ago by Jennifer Pham260
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