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ammawlaammawla/encode-toolkit/skills/scientific-writing/SKILL.md

scientific-writing

Skill20 starsChanged 8 months agoAGPL-3.0View on GitHub

Generate publication-ready methods sections, figure legends, supplementary tables, and data availability statements from ENCODE analysis provenance. Implements the scientific documentation standards requiring complete metadata reporting. Use when the user needs to write methods, generate figure legends, create supplementary tables, draft data availability statements, compile tool citations, or auto-generate any publication text from their ENCODE analysis. Trigger on: methods section, figure legend, supplementary table, data availability, tool citations, publication writing, manuscript, write methods, methods draft, write up, write-up, paper writing, reproducible methods.

41 other projects use a version of this.

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Projects with it also use usfiscaldata, research-grants and 10 more.

Other files people use alongside this one.

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

  • garri333Skill

    research-grants

    Write competitive research proposals for NSF, NIH, DOE, DARPA, and Taiwan NSTC. Agency-specific formatting, review criteria, budget preparation, broader impacts, significance statements, innovation narratives, and compliance with submission requirements.

    Also in 10 projects that use this

  • garri333Skill

    arboreto

    Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets.

    Also in 9 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

  • SoljournerSkill

    get-available-resources

    Enumerate installed packages, databases, and tools for engineering workflows

    Also in 9 projects that use this

  • +7 more from garri333

The file

We split this skill into the rules it gives an agent

6 rules. 0 are common, 6 are distinctive, and 0 are very specific to this project.

  • 0

    Common

    Most of the 38 edited versions we read keep these.

  • 6

    Distinctive

    This author's own choices. Worth a look.

  • 0

    Very specific

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

Licensed with conditions — 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 38 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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