Analyze your own scRNA-seq data!

Steps

  1. Fill in the form
  2. Click "Run Analysis!"
  3. You will be sent to a status page for your run. When the analysis has finished, we'll email you a link to your results page; the status page will also update.

Running the Example Files

  • Matrix: example_flyphone_counts.csv
  • Matrix File Delimitor: 'Space Delimited .CSV' (note that the example counts data is in this format)
  • Metadata: example_flyphone_metadata.csv
  • Or use Seurat Object file: example_flyphone_seurat.rds
  • DEG File (optional): example_flyphone_DEG.csv
  • Control Sample Condition Name: 'Homeostasis'
  • Mutant Sample Condition Name: 'Recovery_d2'

Additional Tips

  • Please ensure that the metadata (.csv) or seurat object (.rds) metadata contains the columns (case-sensitive) "Condition" and "cluster" containing the sample conditions and cell groupings respectively.
  • FlyPhoneDB2 provides the option to compare signaling predictions between two samples/conditions. To enable two condition analysis, ensure the metadata contains both conditions of interest annotated in the Condition column. Additionally, please label the control and mutant samples in the fields under Compare Two Samples. The DEG file is recommended but optional. Example files with recommended formating are provided for each input.
  • Use gene names (eg: csw, wg, indy) as identifiers instead of FBgns
  • Avoid using Gmail account since emails sent from the O2 HPC cluster will likely not be received.
  • Usually an email linking to your result page is sent within a few hours, depending on the size of your data. If you have not received an email within 12 hours, either something went wrong with your run, or we could not reach you by email.

Standalone version is available

Analyze your own scRNA-seq dataset using FlyPhoneDB2 by uploading your data or running the pipeline locally. Click here to download the source code.

Contact Information

Data Upload

Option 1


Example matrix:
- Please check the "Running the Example Files" blurb to the left if you use the example counts & metadata files!



Example metadata:
- Please avoid special characters such as "/ ? +" in the metadata file

Option 2


Example seurat object:
- Please avoid special characters such as "/ ? +" in the metadata file

Compare Two Samples (optional)


Example DEG:
User has the option to upload a DEG file with pre-set cutoff while a DEG file of default setting will be generated and used for filtering if the DEG file is not provided by the user.

Sample names are required for multiple sample analysis and need to be consistent with metadata file or seurat object.



Additional Configurations

  • Version 1: Utilizies Ligand-Receptor pair data from FlyPhone V1.
  • Version 2 High: Utilizes Ligand-Receptor pairs with a "High" rank.
  • Version 2 High/Moderate: Excludes Ligand-Receptor pairs with a "Low" rank.
  • Version 2 All: Utilizes all Ligand-Receptor pairs.

Excludes genes that have a expression percentage below the provided value. Default value is 0.1 (10%).


The number of times to shuffle cluster labels around and compute permutated mean expression averages for p-value scoring. Default value is 1,000.


Note: Uploading large files may take a few minutes.