scPCIP dictionaries and gene -> orthogroup map

Data files used by scPCIP, a program-based cell-type annotator for plant single-cell RNA-seq.

File	Content
gene_to_feature.tsv	gene -> eggNOG orthogroup map for the shipped species (columns species, matrix_gene_id, canonical_id, feature_id, weight, confidence, source)
dictionaries/root.yaml	root programs: epidermis, cortex, endodermis, pericycle, phloem, procambium, xylem, root cap; meristem state
dictionaries/leaf.yaml	leaf programs: epidermis, mesophyll, vasculature (secondary xylem / phloem)
dictionaries/flower.yaml	flower programs: pollen, stamen, carpel, perianth, non-floral
dictionaries/seed.yaml	seed programs: embryo, endosperm, seed coat

Each dictionary lists, per cell type, weighted positive orthogroups learned across many labelled plant single-cell atlases, together with leave-one-species-out reliability estimates (reliability). The scpcip package downloads gene_to_feature.tsv from here on first use; the dictionaries are also bundled with the package.

Species covered by the gene map: Arabidopsis thaliana, Glycine max, Gossypium arboreum, Lotus japonicus, Manihot esculenta, Medicago truncatula, Oryza sativa, Solanum lycopersicum, Solanum muricatum, Sorghum bicolor, Triticum aestivum, Zea mays. Other species can be annotated with a user-supplied map (eggNOG-mapper output).

Citation

Yang, S., Si, C., Wu, Y., Sun, Z., Yao, C., Sun, X., Wang, L., Li, W. & Zhong, Q. scPCIP: cross-species annotation of plant cell types with conserved gene programs. bioRxiv (2026).

License: MIT.