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jaechang-hitsjaechang-hits/SciAgent-Skills/skills/genomics-bioinformatics/etetoolkit/SKILL.md

etetoolkit

Skill386 starsChanged 4 months agoLicence not identifiedView on GitHub

ETE Toolkit (ETE3): Python phylogenetic tree analysis and visualization. Parse Newick/NHX/PhyloXML, traverse/annotate nodes, render figures with TreeStyle/NodeStyle, integrate NCBI taxonomy, run PhyloTree comparative genomics. Use for species trees, gene family evolution, annotated tree figures.

  • Installs packages

11 other projects use a version of this.

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Projects with it also use usfiscaldata, simpy and 7 more.

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Files found in the same public projects as a version of this one, more often than they turn up anywhere else. Each project counts once, large collections count for less, and this file's own repository is left out.
  • yf8578Skill

    usfiscaldata

    Query the U.S. Treasury Fiscal Data API for federal financial data including national debt, government spending, revenue, interest rates, exchange rates, and savings bonds. Access 54 datasets and 182 data tables with no API key required. Use when working with U.S. federal fiscal data, national debt tracking (Debt to the Penny), Daily Treasury Statements, Monthly Treasury Statements, Treasury securities auctions, interest rates on Treasury securities, foreign exchange rates, savings bonds, or any U.S. government financial statistics.

    Also in 7 projects that use this

  • tondevrelSkill

    simpy

    A process-based discrete-event simulation framework. Use for modeling queuing systems, supply chains, manufacturing processes, network simulation, project management, and any system where events occur at specific points in time. Load when working with discrete event simulation, process modeling, resource allocation, virtual time, simpy.Environment, simpy.Resource, or event-driven simulation.

    Also in 8 projects that use this

  • Hongyu-yuSkill

    torch-geometric

    Graph Neural Networks (PyG). Node/graph classification, link prediction, GCN, GAT, GraphSAGE, heterogeneous graphs, molecular property prediction, for geometric deep learning.

    Also in 9 projects that use this

  • ashrafkahoush-uxSkill

    what-if-oracle

    Run structured What-If scenario analysis with multi-branch possibility exploration. Use this skill when the user asks speculative questions like "what if...", "what would happen if...", "what are the possibilities", "explore scenarios", "scenario analysis", "possibility space", "what could go wrong", "best case / worst case", "risk analysis", "contingency planning", "strategic options", or any question about uncertain futures. Also trigger when the user faces a fork-in-the-road decision, wants to stress-test an idea, or needs to think through consequences before committing.

    Also in 6 projects that use this

  • Google DeepMindSkill

    string-database

    Query the STRING database for protein-protein interactions (PPIs), functional enrichment, and homology. Use when the user asks about interactions between specific proteins, interaction evidence, confidence scores, protein interaction partners, or pathway enrichments.

    Also in 7 projects that use this

  • refly-aiSkill

    alpha-vantage

    Get financial data from Alpha Vantage. Use when you need to: (1) retrieve stock quotes and prices, (2) get forex or crypto rates, or (3) access market analytics data.

    Also in 4 projects that use this

The file

We split this skill into the rules it gives an agent

4 rules. 0 are common, 4 are distinctive, and 0 are very specific to this project.

  • 0

    Common

    Most of the 11 edited versions we read keep these.

  • 4

    Distinctive

    This author's own choices. Worth a look.

  • 0

    Very specific

    Tied to their project's names, files or tools. Probably skip.

The licence could not be identified — read it at the source. We count its rules but don't quote them. Read them on GitHub.

“Common” is measured: kept by at least 6 in 10 of the 11 edited versions of this file we could read. “Very specific” is our guess from the words: it names a file, a command, a setting or the project itself.

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