Licensing

I wonder which features of BBrowser are available for free for academic users

Free academic users can access up to 5 public studies in our database, import  Seurat or Scanpy objects, and run almost all downstream analyses in the software (excluding sub-clustering and DE analysis)

What features are restricted under the free user license?

Import file format

What file formats can I import to BBrowser?

You can import FASTQ, MTX, TSV, CSV, .H5, .H5AD, and .RDS files to BBrowser. For details about the structure of each file, please refer to our Documentation section 5_Get your data.

Does BBrowser support importing a dataset downloaded from GEO?

It depends on the format and structure of the file. If the file fulfills all the requirements of the software, you can import it to BBrowser.

Otherwise, if the author of the study is willing to share their annotations, the BioTuring team would be happy to consider hosting the data in our platform and will index the data based on our standard process.

How can I combine multiple datasets?

First, open BBrowser > Data > Add new study to import all files, select your method for batch correction and name the study, then click Start to run the processing. Please refer to our Documentation section 5_Get your data.

How to import an annotation file? Its format?

To import sample info/annotations to the data, you can go to

Color By (to the right of the screen)> click on the drop down button > Add annotation from a file. Here you need to import an annotation file where the 1st column contains the barcodes, and other columns contain the annotations. Please refer to our Documentation section 13_Add an annotation.

Export file format

How can I generate an image for publication?

BBrowser supports exporting multiple graphs: scatter plots, box plots, violin plots, etc. in either SVG or PNG format with a fixed design and layout. You can find the export button at the top right corner of each plot in BBrowser. Please refer to our Documentation section 18_Export Image and data

If you want to customize the color of the graph, go to Settings > Visualization and change the color scale there.

An alternative is to export data of the graph to tsv and reconstruct it by your preferred tools outside BBrowser. BioTuring team also offers a drag-and-drop data visualization tool called BioVinci (www.vinci.bioturing.com). To learn how you can directly export a plot in BBrowser into BioVinci, please refer to our Documentation section 18_Export Image and data

Data export. Is it possible to export a Seurat object from BBrowser??

Exporting Seurat is already in our roadmap. We will let you know as soon as it is ready.

What is the accepted format of a Clonotype file?

To pair clonotype data with expression data, please click on Clonotype (below the screen) and upload the clonotype files. The files should be in TSV/CSV, and should contain the following columns:

Please refer to our Documentation section 17_Study Clonotype.

Methods

How can I compare a gene’s expression in different groups?

To compare gene expression across different clusters:

Please refer to our Documentation section 8_Query gene or protein expression.

What method does BioTuring use for enrichment analysis? 

Each enriched biological process will come with an enrichment score (ES), which is based on Gene Set Enrichment Analysis (GSEA) method. GSEA method can identify classes of genes or proteins that are over-represented in a large set of genes or proteins; these classes can be associated with biological functions or disease phenotypes (Aravind Subramanian et al, 2005).  The package fgsea was used for gene set enrichment analysis in BBrowser. Please refer to our Documentation section 12_Find marker genes and enrichment analysis.

What expression unit does BBrowser use? 

It depends on the unit of each study. For example if your matrix contains UMI counts, by default BBrowser will show the raw UMI counts when you query gene expression. You can change the expression unit to Log2 (raw value) or Log normalized  by going to Settings > Analysis > Gene expression unit. Please refer to our Documentation section 12_Find marker genes and enrichment analysis.

What does the color scale mean when querying multiple genes in BBrowser? 

When you query multiple gene’s expressions (eg. 3 genes), for each cell, we take the sum of 3 genes divided by the sum of all genes. You can refer to this publication for details about the method.

System requirements

My computer has 8GB RAM. Can I process large data?

We recommend using a computer with 16GB RAM for data having more than 100,000 cells or processed from FASTQ file. However, on a computer with 8GB RAM, you can still open large Seurat objects if they are fully processed with PCA and dimensionality reduction results (tested with 300,000-cell object). If you want to submit count matrices, 8 GB RAM can smoothly process data of 30,000 cells. Please refer to our Documentation section 1.2_System requirements

Is there a version of BBrowser Windows on 32 bits ? From the website it seems only possible to use on 64 bits Windows machines.

Unfortunately, BBrowser 2 uses webGL to render graphs, and most analyses require the latest libraries (many of which are only possible to be compiled on a 64 bits system). We don't think the software can work on Windows 32 bits anytime soon. I hope it won't be a big problem for you.

Connection

I got the message “Cannot connect to server”. What can I do?

If you are using a server with a proxy, the message might come up when you try to login to the software since the proxy connection to BioTuring server cannot be made to verify your credentials. Please click on Proxy settings at the bottom of the login screen and configure your server.

Public database

Why is the scatter plot in BBrowser different from the plot in the publication?

Since we cannot obtain all the parameters of the data processing steps from the authors, for some steps, our default parameters may be different from those of the authors.

How often does Bioturing update the pre-processed studies?

 We are curating public studies at the pace of 2.5 studies/ week

Can I merge the data from two projects?

Yes, you could export the expression matrix from each project and upload both files into BBrowser as mtx format with options for batch effect removal.

Are all datasets manually curated by Bioturing, or are they automatically linked from public databases?

At the moment, all datasets on BBrowser are manually curated by the BioTuring Team. We process data using the authors' pipeline and add the annotations to them.

What criteria does BioTuring use to prioritize public datasets for indexing?

We will index a public study if it is

1. Highly requested by users

2. A high-impact study. Immunology and Neuroscience datasets will be prioritized