生物学重复的不同条件下的scrna-seq数据的差异基因表达分析 (https://www.10xgenomics.com/resources/analysis-guides/differential-gene-expression-analysis-in-scrna-seq-data-between-conditions-with-biological-replicates) 需要注意的是,这部分差异表达分析不应与下一部分,计算来自两个簇的细胞之间的差异表达基因以...
However, cell-type identification using marker gene expression could lead to difficulties in distinguishing alternations in the cell-type specification from changes in gene regulation. Identifying cell types using information independent from gene expression, such as lineage tracing, could allow more ...
一张图总结一下CellMarker 2.0数据库概况:👇 3CellMarker 2.0 更新亮点 本次更新的亮点如下:👇 新增36300个tissue-cell type-marker条目、474个组织、1901个细胞类型和4566个marker; 新增48种测序技术分类的细胞marker,包括10×Chromium、Smart-seq2和Drop-seq等; 新增29种细胞Marker,包括蛋白编码基因,lncRNA和p...
Potential doublets were scrutinized using Scrublet from the scran package (1.14.6)66, and marker gene expression was used to assess whether a hybrid transcriptome could mimic the cell type in focus; these analyses did not lead to further removal of cell-associated barcodes. Clustering...
# Check expression of the three genes in the training set. sc.pl.violin(adata_2000, top_3_genes, groupby ='cell_type', rotation =90) mast_cell_weights = weights[model.cell_types =='Plasma cells'] top_3_genes = model.features[mast_cell_weights.argpartition(-3, axis =None)[-3:]]...
Note that theSst44enhancer does not drive gene expression in allCalb2+andHpse+cells (Extended Data Fig.1b,c), indicating thatSst44-enhancer-driven expression overlaps with, but does not strictly mirror, the expression of these marker genes. We therefore refer to the neurons targeted by this ...
Based on the CellTrek result, we can further investigate the co-expression patterns within the cell type of interest using SCoexp module. Here, we will take L5 IT cells as an example using consensus clustering (CC) method. L5 IT cells first are extracted from the charting result. brain_cel...
Lysogen that encodes T7 RNA polymerase. Used to induce expression in T7-driven expression systems relA RNA is synthesized in absence of protein synthesis (relaxed phenotype) relA locus regulates the coupling between transcription and translation. In the wild type, limiting amino acid concentrations re...
FormulaExpressionValues FromMarker FunctionGroup FunctionGroups FutureMetadata FutureMetadataBlock GradientFill GradientStop GradientValues Group GroupByValues GroupItems GroupLevel GroupLevels GroupMember GroupMembers Groups GrowShrinkValues Header HeaderFooter Headers HierarchyUsageType HorizontalAlignmentValues Horizontal...
In the test phase, for a given binary expression profile of the ith cell, bij, we obtain the normalized marker count yi,m defined as.(2)yi,m=1N∑j∈Mmbijwhere Mm is the set of markers of the mth cell type. The cell type is initially determined by taking the maximum of yi,m, i...