AnnData-native toolkit for Plasmodium and VEuPathDB organism bioinformatics.
plasmopack brings the scanpy-style workflow (pp, tl, pl) to malaria and other
non-model eukaryotic pathogens. Query databases, build gene sets, run enrichment, analyse
transcription factors — all without ever leaving your AnnData object.
Status: early development (v0.1.0.dev). API may change before v1.0.
import plasmopack as pp
adata = pp.io.read_h5ad("my_parasite_data.h5ad")
pp.pp.qc_metrics(adata) # QC (apicoplast %, gene counts)
pp.tl.deg(adata, groupby="time") # differential expression
pp.tl.enrich(adata, gene_sets="GO") # pathway enrichment (3 modes)
pp.pl.deg_volcano(adata) # plot — results stay in AnnData
adata.write("annotated.h5ad") # everything saved, self-documenting- Minimum dependencies. Core install needs only
anndata,numpy,pandas,scipy. Everything else is an optional extra — so the package keeps working when the ecosystem changes. - AnnData is the only data model. Every result is written back into standard AnnData slots with full provenance (which database version, which parameters, when).
- Built to last. Fragile data sources ship as versioned offline snapshots; tests never depend on live services.
- VEuPathDB-wide. Plasmodium first, but organism-parameterised from day one (Toxoplasma, Cryptosporidium, Trypanosoma, and more).
pip install plasmopack # core
pip install "plasmopack[all]" # with all optional featuresSee the documentation site (coming soon).
If you use plasmopack, please cite it — see CITATION.cff.
MIT — see LICENSE.
Inspired by plasmoRUtils (R) by Rohit Satyam.