果蝇精巢数据库 http://fly-ted.org/flyted-the-drosophila-testis-gene-expression-database/ 图片.png 12. SynEcoSys https://www.synecosys.cn/#/ SynEcoSys 13. Cell Taxonomy https://ngdc.cncb.ac.cn/celltaxonomy/ Cell Taxonomy
通常是依赖Marker gene来定义每一个类群,可以是GO/KEGG数据库功能富集,虽然这样会比较粗糙,适用于类群不多,而且差异非常大的情形。但是上面例子的细胞类群太多,需要其它方法,通常是根据已经有人整理好的数据库,做如下映射。 这里推荐两个: CellMarker数据库 这里值得推荐的是哈尔滨医科大学 Yun Xiao老师等在2019年1...
Yang K, Ou Q, Li X, Wang P, Zhang Y. CellMarker 2.0: an updated database of manually curated cell markers in human/mouse and web tools based on scRNA-seq data. Nucleic Acids Res. 2023 Jan 6;51(D1):D870-D876.
In my experience, the step which usesminimap2to align reads to the marker gene database uses about 66GB of memory. Output table Marker-MAGuoutputs a long form table, and the combined outputs (fromcombine_sample_tables1.R) are long form. This allows for a smaller file size and nimbler do...
The functional composition of microbial community samples from several environments is predicted based on 16S ribosomal RNA gene sequencing data. Profiling phylogenetic marker genes, such as the 16S rRNA gene, is a key tool for studies of microbial commu
We assembled a database, NeuroExpresso, of publicly available mouse brain cell type-specific gene expression datasets. We then used stringent criteria to select marker genes highly expressed in individual cell types. We found a substantial number of novel markers previously unknown in the literature ...
评价:这个数据库的marker是细胞表面分子marker,和转录组的marker还是不一样。因此不使用。 https://www./cn/resources/cell-markers/immune-cells SCsig: https://www./gsea/msigdb/supplementary_genesets.jsp#SCSig 评价:这是一个基于GSEA分析获得的单细胞测序的marker基因数据集,这个数据集包含的数量比较少。本...
Our purpose was to analyze the immune cell infiltration features and related marker genes for lung cancer.Single cell RNA sequencing data of 11,485 lung cancer cells were retrieved from the Gene Expression Omnibus. After quality control and data normalization, cell clustering was performed using the...
Recent advances have made it possible to analyze high-throughput marker-gene sequencing data without resorting to the customary construction of molecular operational taxonomic units (OTUs): clusters of sequencing reads that differ by less than a fixed dissimilarity threshold. New methods control errors ...
Conclusion Five prognostic marker genes (AC103702.2, LINC00941, CCL11, RPL29P19 and FOXL2) as a gene cluster may serve as prognostic marker genes in HNSCC.doi:10.1111/jop.13186Qilong ZhongDepartment of Ear-Nose-Throat Maoming People's Hospital Maoming ChinaLi Zhou...