An agentic Python framework to curate public single cell data
download/paper_text.txt
download/paper_url.txt
download/study_metadata.txt
download/supp_data/
download/paper_text.txt
download/paper_url.txt
paper_text.txt
and study_metadata.txt
(e.g., citations, dense methods sections).
construct_counts/counts.h5ad
construct_counts/counts.html
qc/qc.h5ad
qc/qc_report.html
qc/qc_params.yaml
qc/qc_params.yaml
to re-run QC with custom values.
transform/transform.h5ad
transform/transform.html
type_cells/type_cells.h5ad
type_cells/type_cells.html
type_cells/type_cells_metadata.yaml
type_cells/type_cells_metadata.yaml
to re-run cell typing with corrected values.
latch_subject_id
latch_condition
latch_disease
latch_tissue
latch_sample_site
latch_sequencing_platform
latch_organism
harmonize_metadata/harmonize_metadata.h5ad
harmonize_metadata/harmonize_metadata.html
--use-params
and --use-metadata
flags to iterate on automated decisionschat
command to understand what went wrong--use-params
--use-metadata