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CellRank 2 reproducibility

CellRank 2’s reproducibility repository

PseudotimeKernel

Hematopoiesis - DPT
Hematopoiesis - Initial state identification
Hematopoiesis - RNA velocity
VelocityKernel vs. PseudotimeKernel - TSI
Cross boundary correctness score

CytoTRACEKernel

Benchmark
- CytoTRACE runtime comparison
- CytoTRACE vs. CytoTRACEKernel benchmark
Embryoid body development

RealTimeKernel

Analysis of mouse embryonic fibroblasts
Analysis of pharyngeal endoderm development

Metabolic labeling

Intestinal organoid differentiation - Data preprocessing
Intestinal organoid differentiation - Parameter inference
Intestinal organoid differentiation - Fate mapping
Intestinal organoid differentiation - Velocity pseudotime
Intestinal organoid differentiation - Kinetic rate change over (pseudo)time
Intestinal organoid differentiation - RNA velocity with EM model
Classical RNA velocity vs. labeling approach - TSI
Intestinal organoid differentiation - Dynamo velocity for pulse experiment
Fixed point analysis - Chase and pulse experiment
Least action path analysis with Dynamo
Method comparsion

.md

Embryoid body development

Embryoid body development#

The CytoTRACEKernel recovers the differentiation landscape and pattern of embryoid body development.

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CytoTRACE vs. CytoTRACEKernel benchmark

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Embryoid body development - CytoTRACE-based analysis

By Philipp Weiler, Marius Lange, Michal Klein, Dana Pe'er, Fabian Theis

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