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.
Read moreAbout author
zglu
Intro
Zhigang is a computational biologist interested in gene expression and regulation, functional genomics, and drug targets discovery. He works on multi-layered omics data (genomics, transcriptomics, epigenomics, single-cell and spatial transcriptomics), applys machine learning modelling and does large-scale dataset visualisation (eg. web-sharing).
He has knowledge and years of experience in NGS, single-cell and spatial multi-omics, bioinformatics, parasite biology and oncology.
Author's posts
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.
Read moreHow 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 moreData: Integrative Bulk All Life Stages
The analysis was performed before: https://v7test.schisto.xyz/dataused/ where 186 bulk sample data from 6 projects were processed with mapping and count.
Read morePrevious links
As the structure of schisto.xyz has been largely re-designed, data of previous versions are still accessable using the original URLs.
Read moreGenesets between Sm v7 and v10
While there is a hugo improvement in the genome assembly from V7 to V10, the geneset stays largely the same.
Read moreData: Sm Adult scRNA-seq
The processed data (a Seurat object) was downloaded from Wendt et al 2020 Science paper and I did some modifications.
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