in-silico-perturbation-oracle

Virtual gene knockout simulation using foundation models to predict transcriptional changes

2.35x

Quality

33%

Does it follow best practices?

Impact

80%

2.35x

Average score across 3 eval scenarios

Securityby

Passed

No known issues

Optimize this skill with Tessl

npx tessl skill review --optimize ./scientific-skills/Data analysis/in-silico-perturbation-oracle/SKILL.md

Evaluation results

100%

58%

Oncology Target Prioritization Report

Target scoring output format and weights

Criteria

Without context

With context

target_gene column

100%

efficacy_score column

100%

safety_score column

100%

druggability_score column

100%

novelty_score column

100%

overall_score column

100%

recommendation column

100%

Efficacy weight 0.35

100%

Safety weight 0.25

100%

Druggability weight 0.25

100%

Novelty weight 0.15

100%

Standard cell type name

100%

Valid perturbation_type

100%

87%

43%

Transcriptomics Pipeline for Cardiac Gene Perturbation Study

Differential expression and pathway enrichment output format

Criteria

Without context

With context

gene_symbol column

100%

log2_fold_change column

100%

p_value column

100%

adjusted_p_value column

100%

perturbed_gene column

100%

cell_type column

100%

pval threshold 0.05

100%

logfc threshold 1.0

100%

Wilcoxon method

fdr_bh correction

70%

Pathway JSON database key

100%

Pathway entry fields

30%

100%

KEGG or GO_BP included

100%

55%

37%

Synergy Screening for Combination Immunotherapy Targets

Combinatorial knockout and QC best practices

Criteria

Without context

With context

predict_combinatorial_ko usage

100%

gene_pairs parameter

100%

synergy_threshold parameter

100%

Negative controls included

16%

33%

Gene vocabulary check

40%

Cell type distribution check

37%

Cross-model validation

30%

Standard cell type name

100%

predict_dose_response usage

18%

export_validation_guide usage

Valid perturbation_type

100%

Repository: aipoch/medical-research-skills
Commit: ca9aaa4

Evaluated: about 1 month ago
Agent: Claude Code
Model: Claude Sonnet 4.6

Table of Contents

Oncology Target Prioritization Report Transcriptomics Pipeline for Cardiac Gene Perturbation Study Synergy Screening for Combination Immunotherapy Targets

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