单细胞测序可用于trajectory analysis探索细胞发育和分化过程,但是由于测序平台的技术限制,测序过程中通常会有偏好地遗漏部分细胞类型。这为精准的trajectory分析带来了巨大挑战,关键细胞类型的缺失往往导致trajectory的中断。而bulk测序不受过度复杂的生物实验影响,能够测得所有细胞的总RNA,因而bulk数据是具有缺失的细胞信息的。
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
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). Analysis steps Step 1. Export projection and clusters from Loupe Browser ...
Single cell trajectory detection. Contribute to dpeerlab/Palantir development by creating an account on GitHub.
Use hodge decomposition for trajectory analysis single-cellsimplicial-complextrajectory-inferencehodge-laplacianhodge-laplacian-decomposition UpdatedFeb 8, 2025 Python Mirror of the Bioconductor package CellTrails (http://bioconductor.org/packages/CellTrails/) ...
Global alignment of complex pseudotime trajectories between different single-cell RNA-seq datasets is challenging, as existing tools mainly focus on linear alignment of single-cell trajectories. Here we present CAPITAL (comparative analysis of pseudotime trajectory inference with tree alignment), a method...
One of the major challenges in single-cell data analysis is the determination of cellular developmental trajectories using single-cell data.Although substantial studies have been conducted in recent years,more effective methods are still strongly needed to infer the developmental processes accurately.This ...
Current methods for analyzing single-cell datasets have relied primarily on static gene expression measurements to characterize the molecular state of individual cells. However, capturing temporal changes in cell state is crucial for the interpretation o
In this research, we developed SigRM, a novel analysis framework for effectively mining single-cell epitranscriptomics datasets deriving from thousands of cells. SigRM not only outperforms state-of-the-art models in RNA methylation site detection on both simulated and real datasets but also provides...
home: https://github.com/KlugerLab/GeneTrajectory-python summary: Compute gene trajectories description: | Gene Trajectory is a Python package that computes and analyzes gene trajectories in single-cell data. It provides tools for trajectory inference, gene expression analysis along trajectories, ...