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Build your own expression explorer with OmicsEE

OmicsEE is a browser-based application designed to facilitate the interactive exploration of omics expression data across multiple atlases.

Data: Sm miracidium and sporocyst scRNA-seq

Single-cell datasets for S. mansoni miracidia (20K cells) and D5 sporocysts (601 cells) are available now!

Data: Sj bulkRNA larval stages

S. japonicum bulk RNA-seq covering larval stages from Cheng et al 2022. Data was mapped to the HuSjv3 genome and TPM was used for normalization.

Data: Sj BulkRNA 14-28d

Raw sequencing data from Wang et al 2017 were downloaded and re-mapped to HuSjV2 genome. Normalised expression based on library-size and gene length were calculated using edgeR.

Data: planarian spatial multiple sections

The study provided multiple Visium sections for Schmidtea mediterranea at 0hpa. On the scanpy data I modified the spatial coordinates for a better view, and also constructed their 3D structure.

How to Cite

While the schisto.xyz database includes an original integrative analysis of bulk RNA-seq data, most datasets are collected from external studies, for which the original publications should be cited.