Interactive exploration of schistosome expression data

public and re-analyzed; multi-species; at the levels of bulk, single-cell, and spatial (ITF) atlases!

Explore Schisto.xyz V2

New Features

Interactive viz

(Multiple) Gene queries, flexible embeddings and metadata.

Web sharing

Share the current visualization state easily in a URL.

Smart search

Fast expression exploration in multiple datasets simultaneously.

Schisto.xyz is now more powerful and interactive.

Serving schisto researchers since 2018, now offers enhanced datasets, interactive visualisation solutions, and a re-designed powerful search engine.

Multimodal datasets

Bulk RNA-seq for all life stages; integrative re-analysis; single-cell atlases; spatial expression (ITF).

Interactive and sharable

Browser-based interactive visualisation supports multiple queries and embeddings, easy share of states via URLs.

Easy customization

Metadata selection, point colors/sizes, subsetting, distribution and composition plots, all highly customizable.

Powerful search

The search engine has been re-designed to provide an expression overview across multiple datasets, fast and robust.

Robust Search & Expression Overview

Fast visualisation of expression in millions of cells / samples, across multiple datasets, at one time.

Explore your favourite gene

Atlas-level Datasets

Integrative bulk RNA-seq

Integrative bulk RNA-seq

Data as in v7test, plus sTe and sOv, 182 samples. See doc

Life cycle RNA-seq

Life cycle RNA-seq

75 samples (mostly larval) from Buddenborg et al 2023. PMID:37935722

Sm adult scRNA-seq

Sm adult scRNA-seq

Data from Wendt et al 2020 with 43K cells, combined clusters. PMID:32973030

Sm ovary scRNA-seq

Sm ovary scRNA-seq

Data from Moescheid et al 2024 with 2K cells. Pre-release.

Sm somule scRNA-seq

Sm somule scRNA-seq

Data with 3K somule cells from Soria et al 2020. PMID:33339816

Sj adult scRNA-seq

Sj adult scRNA-seq

S. japonicum adult scRNA-seq from Lu et al (in prep) with 60K cells.

Smed scRNA all timepoints

Smed scRNA all timepoints

Planarian 55K cells at different regeneration time, norm counts. PMID:37268637

Smed spatial spots

Smed spatial spots

Slightly modified planarian Visium data of 12 sections, explore. PMID:37268637

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Schisto Species

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Single-cell Atlases

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Life-cycle Timepoints

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Bulk Samples

Latest Doc

Data: planarian spatial multiple sections

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

Read more

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.

Read more
View All Docs

Contact Us

Questions? Adding your data?

Feel free to drop me a message via social media / email / contact form. If you find the resource useful, please cite (for now)

Lu et al, bioRxiv 308213 (2018) https://doi.org/10.1101/308213
SchistoXYZ (schisto.xyz)