A. et al. Unsupervised Trajectory Analysis of Single-Cell RNA-Seq and Imaging Data Reveals Alternative Tuft Cell Origins in the Gut. Cell Syst, doi:10.1016/j.cels.2017.10.012 (2017).Herring, C. A. et al. Unsupervised trajectory analysis of single-cell rna-seq and imaging data reveals ...
文献分析 tradeSeq Trajectory-based differential expression analysis for single-cell sequencing data 原文pdf连接 https://www.nature.com/articles/s41467-020-14766-3#Sec23 摘要 轨迹推断通过研究基因表达的动态变化,从根本上增强了单细胞 RNA-seq 研究。在轨迹推断的下游,重要的是发现(i)与轨迹中的谱系相关的...
Single-cell RNA-seq tends to produce noisy data requiring long analysis pipelines in order to glean biological insight. While “all-in-one” tools that simplify this analysis may be attractive from a user’s standpoint, they are not guaranteed to offer the best methods for each individual step...
If you would like to use your own Single Cell Gene Expression data to run the velocity analysis in this guide, you need theoutput directoryfrom Cell Ranger (including theouts/subdirectory). Step 1. Export projection and clusters from Loupe Browser ...
Alessandrini A. Trajectory Analysis Of Single Cell RNAseq Data Suggest Intrarenal Induction Of Tregs In Spontaneously Accepted Kidney Allografts [abstract].Am J Transplant.2022; 22 (suppl 3). https://atcmeetingabstracts.com/abstract/trajectory-analysis-of-...
文献:Computational methods for trajectory inference from single-cell transcriptomics 二、降维方法 降维的方法包括线性降维PCA,ICA等,和非线性降维TSNE,UMAP,DF等。在学习轨迹分析之前,先来了解两种之前接触的比较少的降维方法:ICA和DF。 1. ICA (Independent Component Analysis)独立成分分析 ...
Single cell trajectory analysis is a computational approach that orders cells along a pseudotime axis. This temporal modeling approach allows the characterization of transitional processes such as lineage development, response to insult, and tissue regeneration. The concept can also be applied to resolve...
利用单细胞转录组测序(single-cell RNA-seq)技术对相应的样本进行测序后,就可基于单细胞测序数据具体研究不同细胞状态间的转换过程,中文常称作细胞轨迹的构建或拟时间序列的构建,英文叫cell trajectory/lineage and pseudotime reconstruction/inference。其中pseudotime,中文翻译为拟时间, 一种假定的时间序列。这种类型的单...
https://github.com/seandavi/awesome-single-cell (2018); https://doi.org/10.5281/zenodo.1294021 Zappia, L., Phipson, B. & Oshlack, A. Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database. PLoS Comput. Biol. 14, e1006245 (2018) Bendall, S. C. et ...
We combine the depth of single-cell mass cytometry and an algorithm developed to leverage this continuum by aligning single cells of a given lineage onto a unified trajectory that accurately predicts the developmental path de novo. Applied to human B cell lymphopoiesis, the algorithm (termed ...