SecActPy provides a command line interface for common workflows.
# Bulk RNA-seq (differential expression)
secactpy bulk -i diff_expr.tsv -o results.h5ad --differential -v
# Bulk RNA-seq (raw counts)
secactpy bulk -i counts.tsv -o results.h5ad -v
# scRNA-seq with cell type aggregation
secactpy scrnaseq -i data.h5ad -o results.h5ad --cell-type-col celltype -v
# scRNA-seq at single cell level
secactpy scrnaseq -i data.h5ad -o results.h5ad --single-cell -v
# Visium spatial transcriptomics
secactpy visium -i /path/to/visium/ -o results.h5ad -v
# CosMx (single-cell spatial)
secactpy cosmx -i cosmx.h5ad -o results.h5ad --batch-size 50000 -v
# Use GPU acceleration
secactpy bulk -i data.tsv -o results.h5ad --backend cupy -v
# Use CytoSig signature
secactpy bulk -i data.tsv -o results.h5ad --signature cytosig -v| Option | Description |
|---|---|
-i, --input |
Input file or directory |
-o, --output |
Output H5AD file |
-s, --signature |
Signature matrix (secact, cytosig) |
--lambda |
Ridge regularization (default: 5e5) |
-n, --n-rand |
Number of permutations (default: 1000) |
--backend |
Computation backend (auto, numpy, cupy) |
--batch-size |
Batch size for large datasets |
-v, --verbose |
Verbose output |