scATrans

scATrans is a Python package for mechanism-aware single-cell differential analysis. A standard differential expression (DE) step defines which genes changed; scATrans partitions those genes into transcription-driven versus stabilization-driven classes using the nascent (unspliced) RNA residual—a distinction that total-count fold change alone cannot resolve.

Component	Role
DE	Gene-list membership
Mechanism annotation	Residual-based transcription vs. stabilization labels
Detection (optional)	`add_nascent_score=True` adds active-transcription scores; does not drive mechanism labels

The primary workflow requires spliced and unspliced layers (or mature and nascent layers, e.g. from kb-python) and is most informative at the pathway or program level. The package also supports conventional DE without nascent layers (scanpy, PyDESeq2 pseudobulk, linear mixed models, optional Memento), enrichment (ORA, GSEA, GO, KEGG), and plotting.

Full documentation: Read the Docs.

Requirements

Python 3.10+
AnnData object with a condition column in .obs
For mechanism analysis: spliced/unspliced or mature/nascent layers

Installation

pip install scatrans
# or: conda install -c conda-forge -c bioconda scatrans

Optional extras (scVelo, gene-feature CLI, PyDESeq2, Memento, GSEA) and development installs: installation guide.

Quickstart

import scatrans as scat

result = scat.partition_de_by_mechanism(
    adata,  # AnnData with spliced/unspliced or mature/nascent layers
    groupby="condition",
    target_group="Disease",
    reference_group="Control",
    organism="mouse",
    de="builtin",  # method name, kwargs dict, DataFrame, or callable
    # sample_col="sample",  # preferred when biological replicates exist
    # add_nascent_score=True,  # optional detection columns
    gene_sets=my_pathways,  # optional program-level table
    # induction_matched=True,  # induction-controlled program tests
)
result.regime    # reliability pre-flight (global unspliced fraction)
result.selected  # DE-selected genes with soft mechanism annotation
result.programs  # program-level table when gene_sets is provided
result.summary() # program-first overview

Status

scATrans is 0.10.x (Beta). Prefer import scatrans as scat and names in scatrans.__all__, scat.pl, and scat.qc. See API stability.

Citation

If you use scATrans in published work, cite the software via the Zenodo DOI above and the manuscript when available. See CITATION.cff.

License

Software: Apache License 2.0. Bundled gene-set data (GO, KEGG) may carry separate terms; see the license page before commercial redistribution.

Author

Zhao Li (李钊)
Email: leelieber@gmail.com

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