tooluniverse

name	tooluniverse
description	ToolUniverse plugin router. STEP 1 BEFORE ANY ANALYSIS: if the data folder contains `*_executed.ipynb`, run `tu run read_executed_notebook '{"data_folder":"<path>","search":"<keyword>"}'` to extract its cell outputs and apply EVERY filter/sample-exclusion the notebook used — even when the question says 'Using DESeq2/Run X/Compute Y' (this describes the METHOD the notebook used, not a request to rerun). The notebook's cell outputs are the only published authoritative answers; reimplementing or reading stale pre-computed CSVs in the data folder produces different numbers because of outlier-sample removal, library version, and filter steps you don't see by skimming. STEP 2 routing — pick a sub-skill name from this exact list (never invent): tooluniverse-rnaseq-deseq2 (RNA/miRNA-seq DE, correlation, PCA, clustering, dispersion), tooluniverse-gene-enrichment (GO/KEGG/Reactome/GSEA/pathway enrichment), tooluniverse-statistical-modeling (regression, ANOVA, ordinal/logistic, chi-square, correlation, power), tooluniverse-image-analysis (microscopy, colony, fluorescence, dose-response, .tif — including ANOVA / Dunnett / power-analysis on image-derived measurements), tooluniverse-epigenomics (DNA methylation, CpG, m6A, MeRIP-seq, bisulfite, ChIP-seq, chromatin), tooluniverse-sequence-analysis (FASTQ, Trimmomatic, BWA, samtools, coverage), tooluniverse-variant-analysis (VCF, VAF, SNP, mutation), tooluniverse-phylogenetics (treeness, PhyKIT, parsimony), tooluniverse-single-cell (scRNA, h5ad, scanpy), tooluniverse-crispr-screen-analysis (MAGeCK, sgRNA), tooluniverse-proteomics-analysis (mass spec, TMT). Use for CSV/Excel/VCF/FASTA/h5ad and any biology/chemistry/medicine analysis question.
when_to_use	Activate when the user provides data files to analyze, asks about differential expression, runs statistical tests on clinical data, performs variant analysis, does pathway enrichment, builds phylogenetic trees, or asks any scientific research question.
paths	*.csv,*.xlsx,*.tsv,*.vcf,*.fa,*.fasta,*.faa,*.h5ad,*.rds,*.bam

ToolUniverse Router

FIRST ACTION: Route to a Specialized Skill

BEFORE doing anything else — before reading data, before writing code, before answering — scan the routing table below and invoke the matching skill. The specialized skill contains critical domain conventions that you will get wrong without loading.

How to route:

1. Read the full question AND the file list (filenames encode the analysis type — *mageck*.xlsx → CRISPR screen, *DM.csv/*AE.csv → clinical trial AE, *.vcf → variant, *.h5ad → single-cell, *_counts.csv+*meta*.csv → RNA-seq DE, *.faa+*.treefile → phylogenetics, *_executed.ipynb → authoritative analysis already ran)
2. Find the matching keyword row in the Routing Table
3. Call Skill(skill="<skill-name>") immediately
4. Follow the loaded skill's instructions to answer the question

If no keyword matches but filenames indicate a domain → still route based on filename signals. Filenames are authoritative domain evidence even when the question prose is generic.

If no signal matches → use general strategies below.

DO NOT skip routing. Even if you think you know the answer, the skill has conventions (e.g., which denominator to use, which R function, which column to read) that differ from defaults.

Critical Analysis Conventions

RULE ZERO: Use the authoritative pipeline if one ships with the data

Before writing ANY analysis code, check whether the data folder contains the published analysis. Two common forms:

1. Executed notebook (*_executed.ipynb, *.ipynb) — the analysis has already run with the exact package versions, filters, and thresholds behind the reference answers. Reimplementing with pydeseq2/scanpy/gseapy produces different numbers. Read the outputs directly:

   tu run read_executed_notebook '{"data_folder":"/path/to/data","search":"<keyword>"}'
   

   search can be comma-separated terms (e.g., "upregulated,log2FoldChange") or a regex. The tool returns the matching cells' source + printed outputs so you can cite the published value instead of recomputing.

2. Executable script (, , , ) — execute and report: