can i export the table of results or just the plots?
• 1 views
•
link
written
by
nathanlee •
Tool: BioVinci: user-friendly software to make plotting easy - PCA, 3D scatter plot, venn diagram, you name it.
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
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
• 23,532 views
•
link
updated
by
Ram
•
written
by
Jennifer Pham
•
written
by
Jennifer Pham
3 answers
guys, here's a quick guide on t-SNE in BioVinci:
• 1 views
•
link
written
by
Jennifer Pham
yes, sure. In tsv files
• 1 views
•
link
written
by
Jennifer Pham
Yes @Shannon, you can apply log scale for the axes.
• 0 views
•
link
written
by
Jennifer Pham
Please use the ADD COMMENT and ADD REPLY button instead of posting new answers for upcoming questions. Please add the comments that you gave as answers to the respective questions of the user that asked for it and then remove the answers so that the thread remains organized.
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
• 1 views
•
link
written
by
Jennifer Pham
Log in to answer this question.
More posts like this
-
Tool: PyComplexHeatmap: a Python package to visualize multimodal genomics data
written by Wubin •
-
nucmer and promer plots generated via mummerplot look identical?
written by Jennifer •
-
News: A webinar about UMAP by its author
written by Jennifer Pham
-
Tool: rBCS & pyBCS: open-source packages to support interactive visualizations of single-cell data
written by Jennifer Pham
-
News: [Webinar] Using t-SNE for data analysis : An Introduction by Dr. Laurens van der Maaten (Inve…
written by Jennifer Pham
-
Tool: BioTuring Big Data: a new portal for reanalyzing large public single-cell RNA-seq data sets
written by Jennifer Pham
-
Tool: Hera-T: an efficient and accurate algorithm for quantifying single-cell UMI count data
written by Jennifer Pham
-
How to make k-means clustering plot for relative expression?
written by ahmad mousavi
-
Per base sequence quality and per base N content
written by misterie
-
Blog: Workshop recording from NYU Langone Medical Center on Machine Learning for Transcriptomics da…
written by elia.brodsky
An enhancement : a function to transform the input matrix.
hi Zhilong, BioVinci can now transform the input matrix well for data with replications. Is it what you refer to?
Seems like a UI for R. Can it plot the 3D PCA and biplots?
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.
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?
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:
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:
seems pretty, but what linux do you support?
we support ubuntu 16.04 and 18.04 LTS
@nathanlee: we support ubuntu 16.04 and 18.04 LTS
Is this a commercial product?
Yes, it is. But I believe it will help you save a lot of time for PCA, t-SNE, and other advanced analyses.
It may well do so, but I think we have rules about posts about commercial products.
hi Alex, could you suggest any reference for posts about commercial products so that I can do it right?
thanks, the 3d pca looks great.
i mean the pca or tsne results
why not use R? It's free and does anything you want.
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.
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.
thanks for your answer!
That violin plot looks awesome. Is there a way to apply log scale for the data?
Yes @Shannon, you can apply log scale for the axes.
The biplot seems not quite right.
@nathanlee: I got it. The origins of the inner axes should have overlapped on each other. Yet you can adjust this in BioVinci