Recent advances in single-cell technologies have enabled high-throughput molecular profiling of cells across modalities and locations. Single-cell transcriptomics data can now be complemented by chromatin accessibility, surface protein expression, adapti
We developed DREAMIT (Dynamic Regulation of Expression Across Modules in Inferred Trajectories) to annotate transcription-factor activity along single-cell trajectory branches, using ensembles of relations to target genes. Using a benchmark representing several different tissues, as well as external ...
Also, no trajectory inference method provides the possibility to map new cells to previously obtained reference trajectories without pooling cells and re-computing trajectories. To fill these gaps, we have developed STREAM (Single-cell Trajectories Reconstruction, Exploration And Mapping), a comprehensive...
Single-cell sequencing assay for transposase-accessible chromatin (scATAC-seq) is the state-of-the-art technology for analyzing genome-wide regulatory landscapes in single cells. Single-cell ATAC-seq data are sparse and noisy, and analyzing such data is
Single-cell assay is an ensemble of genomics, transcriptomics, proteomics and metabolomics to study a system at a single cell level.
Single-cell ATAC-seq (scATAC-seq) technology has also been developed to study cell type-specific chromatin accessibility in tissue samples containing a heterogeneous cellular population. However, due to the intrinsic nature of scATAC-seq data, which are highly noisy and sparse, accurate extraction ...
个人非常喜欢的 RNA velocity,利用 splicing 引入真实的 cell transition 方向。 Image 与之前那些 monocle 等基于表达谱相似来构造 trajectory 的不同,RNA velocity 是利用转录这一天然的蕴含时间的过程来对 Cell transition 有个刻画。 Image CellRank:思路也很自然结合两者,RNA velocity + 表达谱相似,从而对细胞的 ...
pinellolab / STREAM Star 174 Code Issues Pull requests STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data visualization python scrna-seq lineage trajectory singlecell scatac-seq Updated Dec 18, 2021 Jupyter Notebook ...
2017年7月,奥地利研究人员在Nature Methods上发表“Pooled CRISPR screening with single-cell transcriptome readout (doi:10.1038/ nmeth.4227)”文章,创造性地将CRISPR-Cas9和单细胞RNA测序两种极有前景的基因组学领域结合在一起,发明了这种被称作CROP-seq的单细胞测序方法 (CRISPR droplet sequencing, CRISPR液滴测...
[12]. At the cell level, cell-cell communication offers speculation from the perspective of cellular interactions [13] while cell trajectory analysis incorporates the temporal information (Fig.1A) [14]. Furthermore, inferring copy number variations (CNVs) with inferCNV analysis by comparing gene ...