Phenosuite
F 38 completed
Other
containerized / r · small
91
Files
23,820
LOC
0
Frameworks
7
Languages
Pipeline State
completedRun ID
#1429385Phase
doneProgress
0%Started
2026-04-16 07:44:08Finished
2026-04-16 07:44:08LLM tokens
0Pipeline Metadata
Stage
CatalogedDecision
proceedNovelty
47.00Framework unique
—Isolation
—Last stage change
2026-05-10 03:34:46Deduplication group #51636
Member of a group with 37 similar repo(s) — canonical #1208548 view group →
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🧪 Code Distillation
Browse all specs →Sample distilled functions (click for full spec)
pcf_AUCGenerates and returns a pandas DataFrame summarizing interaction results by calculating and visualizing the distribution of normalized Pairwise Correlation Factors (PCFs) between a specified cell type and all other cell types. It accepts a DataFrame containing PCF data, lists of cell types, the prim
plot_pcf_curvesComputes and aggregates pairwise interaction data across specified cell types. It takes a primary data frame, a list of cell types, a resolution parameter, a label, an output path, and a radius value as inputs. The function iteratively calculates interaction subsets for every pair of cell types, com
plot_differenceGenerates a visualization comparing two sets of data by plotting the median of the normalized PCF values against the x-axis data. It accepts a data structure containing the necessary PCF measurements and an optional boolean flag to control figure creation. The function outputs a matplotlib axes obje
AI Prompt
Create a containerized, integrated bioinformatics platform for single-cell spatial omics analysis, similar to PhenoSuite. I need it to be built using R Shiny and Docker Compose so I can run it with a single command. The platform must include modules for spatial transcriptomics (like MERFISH), multi-modal data integration (e.g., CODEX), and cell phenotyping. Specifically, include tools for analyzing, pre-processing, and comparing spatial data objects, and add an automated phenotyping feature powered by an LLM, which requires an OpenAI API key.
r shiny docker bioinformatics spatial-omics containerization sc-analysis merfish data-integration
Generated by gemma4:latest
Catalog Information
Create a containerized, integrated bioinformatics platform for single-cell spatial omics analysis, similar to PhenoSuite. I need it to be built using R Shiny and Docker Compose so I can run it with a single command. The platform must include modules for spatial transcriptomics (like MERFISH), multi-modal data integration (e.g., CODEX), and cell phenotyping. Specifically, include tools for analyzing, pre-processing, and comparing spatial data objects, and add an automated phenotyping feature powe
Tags
r shiny docker bioinformatics spatial-omics containerization sc-analysis merfish data-integration
Quality Score
F
38.5/100
Structure
32
Code Quality
28
Documentation
41
Testing
0
Practices
65
Security
92
Dependencies
80
Strengths
- Good security practices — no major issues detected
- Containerized deployment (Docker)
Weaknesses
- No LICENSE file — legal ambiguity for contributors
- No tests found — high risk of regressions
- No CI/CD configuration — manual testing and deployment
- 11 files with critical complexity need refactoring
- 4435 duplicate lines detected — consider DRY refactoring
- 13 'god files' with >500 LOC need decomposition
Recommendations
- Add a test suite — start with critical path integration tests
- Set up CI/CD (GitHub Actions recommended) to automate testing and deployment
- Add a linter configuration to enforce code style consistency
- Add a LICENSE file (MIT recommended for open source)
Languages
Frameworks
None detected
Symbols
function55
variable5
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BinComp Dependency Hardening
All packages →4 of this repo's dependencies have been scanned for binary hardening. Grade reflects RELRO / stack canary / FORTIFY / PIE coverage.