cell typesRpythonRNA sequencingThe analysis of the single-cell transcriptome has emerged as a powerful tool to gain insights on the basic mechanisms of health and disease. It is widely used to reveal the cellula
Genome-wide identification of single-cell transcriptomic responses of drugs in various human cells is a challenging issue in medical and pharmaceutical research. Here we present a computational method, tensor-based imputation of gene-expression data at t
Contemporary single-cell lineage-tracing (scLT) methods use expressed, heritable DNA barcodes to combine cell lineage readout with single-cell transcriptomics. However, reliance on transcriptional profiling limits adaptation to other single-cell assays. With CellTag-multi, we present an approach that ...
A pan-cancer spatial single-cell transcriptome atlas.aSchematic depicting the study design. The cancer types included in this pan-cancer study were displayed in the first image on the left, created by Figdraw.bThe number of samples in the pan-cancer analysis of scRNA-seq and ST.cPie chart ...
PyMINEr [80] Python An automated tool for cell-type identification, filtering enriched genes, network pathway analysis, and visualization of analysis. Non-cell type determining gene expression may influence cellular graphs.https://www.sciencescott.com/pyminer Pre-processing dropEst [81] R Accurate est...
popular approach, since over 60 benchmarks have been conducted for single-cell data analysis alone (see below and Additional file1). But even if done neutrally, the community may still want a mechanism to challenge, extend, or personalize the assessments (e.g. update/add reference datasets,...
With emergence of single-cell biology and adaptation of various sequencing-based omics technologies, the study of chromatin accessibility at single cell resolution became possible owing to the development of single-cell ATAC sequencing (scATAC-seq). However, computational analysis of scATAC-seq data ...
Somatic embryogenesis is a major process for plant regeneration. However, cell communication and the gene regulatory network responsible for cell reprogramming during somatic embryogenesis are still largely unclear. Recent advances in single-cell technol
The DifferentGeneTest function was used for differential expression analysis, and the top 2000 significant genes were selected to define cell progression. The DDRTree method was used to reduce the dimensions. The pseudotime trajectory was visualized with the plot_cell_trajectory function in the Monocle...
The application of single-cell RNA sequencing (scRNA-seq) in biomedical research has advanced our understanding of the pathogenesis of disease and provided valuable insights into new diagnostic and therapeutic strategies. With the expansion of capacity f