Precomputed ccisignal outputs for CellNeighborEX v2

This dataset provides the precomputed outputs of the ccisignal module from the CellNeighborEX v2 pipeline. It includes two files: [ccisignal_output] sc_ccisignal.h5ad: scRNA-seq reference with cell-type–specific expression[ccisignal_output] sp_ccisignal.h5ad: Visium data with expected expression per spot and geneThe provided outputs cover the datasets used in the manuscript: simulation: synthetic spatial transcriptomics datasethippocampus: mouse brain tissue (derived from Slide-seq)liver cancer: mouse liver tumor tissue (derived from Slide-seq)ovarian cancer: human ovarian tumor tissuecolorectal cancer: human colorectal tumor tissuelymph node: mouse lymph node (infection model; MS: infected, PBS: control)These files are hosted here due to size limitations and are intended to enable reproducibility of the downstream analyses described in the manuscript. Users can set `START_FROM=6` in `run_cnex2.sh` to run the ccigenes and ccipairs modules without rerunning ccisignal.