pseudotime-trajectory-viz
Visualize single-cell developmental trajectories (pseudotime) to show how cells differentiate from stem cells to mature cells. Includes trajectory inference, pseudotime calculation, and publication-ready visualizations.
Install with Tessl CLI
npx tessl i github:aipoch/medical-research-skills --skill pseudotime-trajectory-viz72
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Evaluation results
100%
92%Hematopoietic Differentiation Trajectory Analysis
CLI usage and output file structure
CLI entry point used
0%
100%
analysis_report.json exists
0%
100%
report has method field
0%
100%
report has n_cells field
0%
100%
report has root_cell field
0%
100%
pseudotime_range structure
0%
100%
lineages as dict
0%
100%
pseudotime_values.csv exists
0%
100%
csv has cell_id column
100%
100%
csv has pseudotime column
0%
100%
csv has lineage column
0%
100%
trajectory_plot file
0%
100%
Without context: $0.4337 · 2m 32s · 21 turns · 24 in / 6,424 out tokens
With context: $0.8867 · 3m · 35 turns · 245 in / 7,068 out tokens
100%
86%Stem Cell Marker Dynamics During Hematopoietic Differentiation
Gene expression dynamics along trajectories
genes flag used
0%
100%
plot-genes flag used
0%
100%
gene_trends directory exists
0%
100%
individual gene trend files
0%
100%
requested genes in trend files
0%
100%
gene expression heatmap
100%
100%
scripts/main.py entry point
0%
100%
trajectory_plot exists
0%
100%
analysis_report.json exists
0%
100%
Without context: $0.6140 · 3m 23s · 29 turns · 82 in / 9,750 out tokens
With context: $0.9437 · 3m 17s · 37 turns · 478 in / 7,775 out tokens
95%
91%Cell Cluster Connectivity and Graph-Based Trajectory Analysis
PAGA method and alternative trajectory inference
method paga flag
0%
100%
analysis_report method field
14%
100%
paga_graph file exists
0%
100%
start-cell-type flag used
0%
100%
trajectory_plot exists
0%
100%
pseudotime_values.csv exists
0%
100%
analysis_report.json structure
0%
50%
scripts/main.py entry point
0%
100%
output directory used
25%
100%
Without context: $0.6680 · 3m 30s · 30 turns · 37 in / 10,109 out tokens
With context: $1.5617 · 5m 55s · 44 turns · 9,037 in / 17,730 out tokens
- Evaluated
- Agent
- Claude Code
Table of Contents
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