20 used qualitative inspection of non-linear dimension reduction plots. This can be informative, but is difficult to scale up and make objective. Germain et al.24 compared how well the transformations recovered a priori assigned populations, defined either through FACS or by mixing different cell ...
The number of principal components retained was picked based on the inspection of the “elbow plot” and JackStraw procedure (n=100 replicates, 50 PCs) in Seurat. A UMAP embedding was calculated on the top 12 principal components using the RunUMAP() function with n.neighbors=50, min.dist =...
Tumor protein 53 (TP53) is the most frequently mutated gene in human cancer, typically occurring as a multihit process with a point mutation in one allele and loss of the other wild-type (WT) allele1,2.TP53mutations are also strongly associated with copy number alterations (CNA) and structu...
4. Inspection of results 4.1 Orienting the results Upon completion of the analysis. The folderres/hippo_1folder should contain the following set of files: foo@bar:~$ls -1logits.2019-10-29090750.880065.tsvR.2019-10-29090750.880065.tsvsc_loss.2019-10-29090750.880065.txtsc_model.2019-10-29090750.8...
[19], a gene expression profile (GEP), UMAPs of the results of batch correction, clustering, and cell-type annotation, and files of DEGs and GSEA [23], users can apply sub-clustering for further inspection by repeating this single-cell data analysis procedure on specified clusters of ...
S2a,b). Visual inspection of the data for each time point by using t-SNE and UMPA suggested that there were some overlapping distributions of cells and a similar proportion of cell identities (Additional file 1: Fig. S3a). In addition, distribution of cell numbers and mRNA profiles in ...
(Fig.1b,cand Extended Data Fig.1c–g). These data also integrated coherently with published zebrafish scRNA-seq data from earlier and overlapping timepoints, despite collection on different platforms (Extended Data Fig.1h,i). Cell type identity was inferred by inspection of marker genes for ...
1971Accesses Abstract The automatic analysis of cancer cells has gained increasing relevance given the amount of data that biology researchers have to analyze. However, most biology researchers still analyze cells by visual inspection alone, which is time consuming and prone to induce subjective bias....
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(Method). Initially 49 clusters were obtained with a resolution parameter of 0.15. By manual inspection, several over-clustered cell types, including nine L2/3 IT 1, two L2/3 IT 2, six L4 IT 2, six L6 CT, and two L6 IT 2 clusters were merged, and one spurious cluster was removed,...