CellRank Meets Experimental Time

In this tutorial, you learned how CellRank can be used to compute a transition matrix based on experimental time points and how the transition matrix can be ...

cellrank documentation

Estimate differentiation direction based on a varied number of biological priors, including pseudotime, developmental potential, RNA velocity, experimental time ...

cellrank_notebooks/tutorials/kernels/500_real_time.ipynb at main

CellRank Meets Experimental Time¶. Preliminaries¶. In this tutorial, you will learn how to: match cells across experimental time points using a {class} ~moscot.

consider add more visualization tool for CellRank2 meets ... - GitHub

consider add more visualization tool for CellRank2 meets with experimental timepoint (waddington transport) #1221. Open. LiuCanidk opened this ...

Tutorials - cellrank documentation

Tutorials¶ · CellRank Meets RNA Velocity · CellRank Meets Pseudotime · CellRank Meets CytoTRACE · CellRank Meets Experimental Time.

CellRank Meets CytoTRACE

CellRank Meets RNA Velocity · CellRank Meets Pseudotime; CellRank Meets CytoTRACE; CellRank Meets Experimental Time · Estimators. Toggle navigation of ...

CellRank 2: unified fate mapping in multiview single-cell data - PMC

CellRank 2 provides a set of diverse kernels that derive transition probabilities based on gene expression, RNA velocity, pseudotime, ...

Kernels - cellrank documentation

Kernels¶ · CellRank Meets RNA Velocity · CellRank Meets Pseudotime · CellRank Meets CytoTRACE · CellRank Meets Experimental Time.

CellRank for directed single-cell fate mapping | Nature Methods

Here, we present CellRank, a method that combines the robustness of similarity-based trajectory inference with directional information from RNA ...

API - cellrank documentation

cellrank.estimators use the cell-cell transition matrix to derive insights about cellular dynamics, for example, they compute initial and terminal states, fate ...

CellRank 2: Unified fate mapping in multiview single-cell data

CellRank [Lange et al., 2022, Weiler et al., 2024] is a modular framework to study cellular dynamics based on Markov state modeling of multi-view single-cell ...

Getting Started with CellRank

use CellRank estimators to analyze the transition matrix, including the computation of fate probabilities , driver genes , and gene expression trends . read and ...

CellRank 2: unified fate mapping in multiview single-cell data

Here we present CellRank 2, a versatile and scalable framework to study cellular fate using multiview single-cell data of up to millions of ...

CellRank 2 preprint out - Marius Lange

CellRank 2 comes with a modular interface that makes it easy to learn transition probabilities among cells based on various data modalities or ...

cellrank.pl.log_odds

Plot log-odds ratio between trajectories. This plotting function is geared towards time-series datasets that have been analyzed using the RealTimeKernel . It ...

CellRank for directed single-cell fate mapping - bioRxiv

However, lineage relationships are lost in scRNA-seq due to its destructive nature—cells cannot be measured multiple times. Experimental ...

CellRank for directed single-cell fate mapping - ResearchGate

CellRank also predicts a novel dedifferentiation trajectory during regeneration after lung injury, which we follow up experimentally by ...

Mapping lineage-traced cells across time points with moslin

As expected, pseudotime assignments in both approaches are correlated with experimental time (Supplementary Fig. 7d) [72]. We supply CellRank 2 ...

A toolbox for OT problems in single cell genomics; Primer ... - YouTube

single cell genomics Meeting Moscot: A scalable toolbox for optimal ... For lineage-traced in-vivo time-series experiments, we present ...

CellRank for directed single-cell fate mapping

Abstract. Computational trajectory inference enables the reconstruction of cell state dynamics from single-cell RNA sequencing experiments. However, trajectory ...