Develop an ontology standardized database of published marker gene literature; 2. Develop and apply a marker gene classification algorithm; and 3. Create user interface and input data structure for scRNA-seq cell type prediction.Indiana University - Purdue University Indianapolis.;Indiana University - ...
Gene Expression Visualize the expression of genes and gene sets using a normalized view of our data corpus of over 35 million cells. Explore the tool Annotate Expedite cell type characterization and eliminate communication overhead by empowering tissue experts to directly explore and annotate datasets....
The cell type labels can be supplied as a path to the file containing cell type label per line corresponding to the cells in gene expression data. Any list-like objects (such as a tuple or series) are also acceptable. If the gene expression data is input as an AnnData, you can also ...
Gene-linked peaks were enriched for Enhancer-like Signature (ELS) elements from the ENCODE candidate CRE database42 (Methods; Extended Data Fig. 8k). Genes linked to on-target and off-target DERs displayed fate-specific expression patterns (Fig. 4d and Extended Data Fig. 8l). On-target ...
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The cell type information in all datasets is used for biological conservation evaluation. Identification of signature attentions of cell types and sub-clusters The signature attentions of cell types are identified based on Wilcoxon rank-sum (Mann–Whitney-U) test. Same as scanpy, attention scores ...
- Broséus Jet al. VEGF121, is predictor for survival in activated B-cell-like diffuse large B-cell lymphoma and is related to an immune response gene signature conserved in cancers. Oncotarget (2017) 8(53): 90808-90824 - Delyon Jet al. PDE4D promotes FAK-mediated cell invasion in BRAF...
Using the ‘Transcriptome’ clustering of each sample as the common cell type delineator, we calculated pseudobulk count matrices for the four previously used gene sets – that is, ‘Transcriptome’, ‘Random’, ‘Transcription Factors’ and ‘Core Matrisome’. Taking into account only one-to-...
Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression limix_qtlPublic cellsnp-litePublic Efficient genotyping bi-allelic SNPs on single cells cardelinoPublic Clone identification from single-cell data ...
Single-cell sequencing provides a high-quality genomic picture of an individual cell, rather than a broad genomic snapshot from bulk DNA or RNA sequencing of tissue or sample. Single-cell sequencing is important in gene regulation studies and analyzing differences in gene expression between cells. ...