Upload data and then fill in the fields to generate an executable file required for running scLANE webserver analysis. Additional details are provided below.

Model type: For single-subject/sample data use GLM mode. For multi-subject/sample data, choose one of GEE and GLMM mode, which provide population-level dynamics or sample-specific dynamics, respectively.

Number of basis functions: Controls the maximum complexity of the expression dynamics. We recommend three to cover most dynamic patterns.

Number of highly variable genes: Select how many highly variable genes to test using scLANE. If HVG's have already been identified and saved in the Seurat object, they will be pulled directly. Alternatively, you may submit a vector of genes for testing by naming a list object as HVG in your custom RDS upload.

Random seed: Enter a value for reproducibility.

Pseudotime column: This must be provided in the Seurat object metadata or as a vector in a named list object (enter the object name in this case).

Cell offset column: If provided, this should be in the Seurat object metadata or as a vector in a named list object (enter the object name in this case). If not provided, offsets will be created as counts-per-10k. The offset represents the scaling factor used to account for sequencing depth factor differences across cells.

Subject ID column: If GEE or GLMM mode are selected, then a Seurat metadata column or named list object containing the subject/sample IDs is required.

If using a custom data object, a screenshot demonstrating the required format and minimal requirements is available on GitHub.

Preview of uploaded file or Seurat metadata:

Please report any comments, questions, or issues at Github