FAVA: Functional Associations using Variational Autoencoders
FAVA is a method used to construct protein networks based on omics data such as single-cell RNA sequencing (scRNA-seq) and proteomics. Existing protein networks are often biased towards well-studied proteins, limiting their ability to reveal functions of understudied proteins. FAVA addresses this issue by leveraging omics data that are not influenced by literature bias. Read the documentation.
Data availability
Installation:
pip install favapyfavapy as Python library
Read the How_to_use_favapy_in_a_notebook or/and the documentation. Relevant parameters for fava.cook.
favapy supports both AnnData objects and count/abundance matrices.
Command line interface
Run favapy from the command line as follows:
favapy <path-to-data-file> <path-to-save-output>Optional parameters:
-t Type of input data ('tsv' or 'csv'). Default value = 'tsv'.
-n The number of interactions in the output file (with both directions, proteinA-proteinB and proteinB-proteinA). Default value = 100000.
-c The cut-off on the Correlation scores.The scores can range from 1 (high correlation) to -1 (high anti-correlation). This option overwrites the number of interactions. Default value = None.
-d The dimensions of the intermediate\hidden layer. Default value depends on the input size.
-l The dimensions of the latent space. Default value depends on the size of the hidden layer.
-e The number of epochs. Default value = 50.
-b The batch size. Default value = 32.
-cor Type of correlation method ('pearson' or 'spearman'). Default value = 'pearson'
If FAVA is useful for your research, consider citing FAVA BiorXiv.