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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
Embryoid body development - CytoTRACE-based analysis
Embryoid body development - Initial state identification
Diffusion pseudotime
Palantir pseudotime
RealTimeKernel
Analysis of mouse embryonic fibroblasts
Real-time informed pseudotime on mouse embryonic fibroblasts
Initial state identification for mouse embryonic fibroblasts
Diffusion pseudotime on mouse embryonic fibroblasts
Palantir pseudotime on mouse embryonic fibroblasts
WOT-based analysis of mouse embryonic fibroblasts
RNA velocity analysis on mouse embryonic fibroblasts
VelocityKernel vs. RealTimeKernel - TSI
Analysis of pharyngeal endoderm development
Pharyngeal endoderm development analysis with the RealTimeKernel
Initial state identification on full pharyngeal endoderm development data
Pharyngeal endoderm development analysis with RealTimeKernel
Initial state identification on subsetted pharyngeal endoderm development data
Pharyngeal endoderm development analysis with WOT
Pharyngeal endoderm development analysis with the RealTimeKernel
Pharyngeal endoderm development analysis with the RealTimeKernel
VelocityKernel vs. RealTimeKernel - TSI
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
Index