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xlsx

Create, edit, analyze, or convert Excel spreadsheets (.xlsx, .xlsm, .xltx) where the workbook file is the primary deliverable. Use for formulas, formatting, financial models, multi-sheet workbooks, and tabular cleanup exported to Excel. Also applies to .csv/.tsv when the user wants spreadsheet output. Do NOT use for Word documents, HTML reports, standalone Python scripts, database pipelines, or Google Sheets API work.

Qu'est-ce que xlsx ?

xlsx is a Claude Code agent skill that create, edit, analyze, or convert Excel spreadsheets (.xlsx, .xlsm, .xltx) where the workbook file is the primary deliverable. Use for formulas, formatting, financial models, multi-sheet workbooks, and tabular cleanup exported to Excel. Also applies to .csv/.tsv when the user wants spreadsheet output. Do NOT use for Word documents, HTML reports, standalone Python scripts, database pipelines, or Google Sheets API work.

Compatible avecClaude Code~Codex CLI~Cursor
npx skills add https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/xlsx

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Documentation

XLSX creation, editing, and analysis

TaskApproach
Create or edit with formulas/formattingopenpyxl — see gotchas below
Bulk data in or outpandas (read_excel, to_excel)
Quick look at a sheetmarkitdown file.xlsx## SheetName per sheet; reads .xlsm too. No cell coordinates, so don't plan edits from it
Read a model (formulas and values)two load_workbook passes — see gotchas

openpyxl, pandas, and markitdown are preinstalled — do not run uv pip install first; write the script and import directly. Only if an import fails (or the markitdown command is missing): uv pip install the missing package.

Script paths below are relative to this skill's directory.

Requirements for every output

  • Professional font (Arial, Times New Roman) throughout, unless the user says otherwise.
  • Zero formula errors. Never ship while recalc.py reports errors_found. If you think an error predates you, prove it: load the original with data_only=True and look at that cell. An error you introduced looks exactly like one you inherited.
  • Use formulas, never hardcoded results. Write sheet['B10'] = '=SUM(B2:B9)', not the Python-computed total. The sheet must recalculate when its inputs change.
  • Follow the user's spec literally. Exact tab names, exact column headers, and the formula they spelled out. A redesign that computes something else fails, however elegant.
  • Document every assumption and hardcoded number where the reader will see it — a cell comment, or an adjacent cell at a table's end. Cite a real source when one exists (Source: Company 10-K, FY2024, Page 45, Revenue Note, [SEC EDGAR URL]); when the number came from the user, say so plainly.
  • A workbook you create for someone to fill in needs a short legend naming which cells to edit, and one example row of realistic values showing the expected format. Never add such a row to a file you were asked to edit.
  • Editing an existing file: match its conventions exactly. They override every guideline here. Find its designated input cells first — a distinct font color, fill, or shading marks them — write only there, and leave every existing formula untouched.

Recalculate (mandatory whenever the file contains formulas)

openpyxl writes formulas as strings with no cached values. Until you recalculate, every formula cell reads back as None to anything reading cached values — pandas, load_workbook(data_only=True), and most previewers.

python scripts/recalc.py output.xlsx [timeout_seconds]   # default 30

LibreOffice computes every formula, the file is rewritten in place, and you get JSON: status (success | errors_found), total_formulas, total_errors, and an error_summary naming up to 100 cells per error type (locations_truncated says how many it withheld — trust total_errors, not the length of the list). Fix what it names and run it again. JSON with an error key instead of a status means nothing was recalculated, and only that case exits non-zero — errors_found exits 0, so never treat a clean exit as a clean workbook.

A green recalc proves your formulas evaluate, not that they are right. An off-by-one range or a reference to the wrong row yields a clean, error-free file with wrong numbers. Write 2–3 formulas first and check they pull the values you expect, before building out a grid.

A workbook that links to another file loses those links if you re-save it with openpyxl and then recalculate. Such a formula reads ='[1]Returns Analysis'!$B$2 — the [1] is an index into the workbook's external-reference list, naming a separate file on disk, not a sheet. That file is rarely present here, so the cell's cached value is the only thing holding its data. openpyxl strips that value on save; LibreOffice then has to resolve the reference for real, fails, writes #NAME?, and deletes every link. recalc.py refuses to run in that state — copy those cells' values out of the original before you save over them (--force overrides, and accepts the loss).

Choosing formulas that survive verification

LibreOffice implements fewer functions than Excel, and one it cannot evaluate becomes a literal #NAME? baked into the file you deliver.

  • Prefer Excel-2007-era functionsSUMIFS, INDEX, MATCH, IFERROR, SUMPRODUCT — which need no prefix.
  • Six post-2007 functions work, but only with an _xlfn. prefix, because openpyxl writes your formula into the XML verbatim and Excel stores post-2007 names prefixed (its UI hides the prefix): _xlfn.TEXTJOIN, _xlfn.CONCAT, _xlfn.IFS, _xlfn.SWITCH, _xlfn.MAXIFS, _xlfn.MINIFS. Written bare, each yields #NAME?.
  • Never use XLOOKUP, XMATCH, SORT, FILTER, UNIQUE, or SEQUENCE. The runtime's LibreOffice cannot evaluate them under any prefix. Newer builds do evaluate them, but they are spilling array functions and an openpyxl-written file has no spill metadata, so only the top-left cell of the range gets a value — and recalc.py reports total_errors: 0 on the truncated result. Use INDEX/MATCH for lookups, and sort, filter, and de-duplicate in Python before writing the cells.
  • A formula LibreOffice could not parse is written back lowercased — a quick tell beside a #NAME?.

openpyxl gotchas

  • Reading a model takes two loads. data_only=True yields cached values with the formulas gone; the default yields formula strings with no values. One pass cannot give you both.
  • data_only=True is destructive if you save. That workbook has no formulas left, so saving replaces every one with a literal — permanently.
  • data_only=True on a file openpyxl just wrote returns None everywhere — run recalc.py first. (A formula whose result is "" also reads back as None.)
  • Merged cells: write the top-left anchor only. Every other cell in the range is a MergedCell whose .value is read-only.
  • .xlsm loses its macros unless you pass keep_vba=True to load_workbook.
  • A sheet name containing a space must be quoted in a cross-sheet reference: ='Assumptions Inputs'!$B$5. Unquoted, it evaluates to #VALUE!.

Financial models

Unless the user says otherwise, or the existing file already does something else.

Color: blue text (0,0,255) for hardcoded inputs and scenario levers · black for formulas · green (0,128,0) for links to another sheet · red (255,0,0) for links to another file · yellow fill (255,255,0) for key assumptions and cells the user should fill in.

Numbers: currency $#,##0, with the unit named in the header (Revenue ($mm)) · zeros render as -, including in percentages ($#,##0;($#,##0);-) · negatives in parentheses · percentages 0.0%, stored as fractions (0.15 renders 15.0%; storing 15 renders 1500.0%) · valuation multiples 0.0x · years as text ("2024", never 2,024).

Structure: every assumption in its own labeled cell, referenced by the formulas that use it (=B5*(1+$B$6), never =B5*1.05) · formulas consistent across every projection period, since a lone edited cell mid-row is the commonest silent error · guard denominators that can be zero.

Dependencies

openpyxl, pandas, markitdown (pip, preinstalled — install only if an import fails or the command is missing) · LibreOffice (soffice, auto-configured for sandboxed environments via scripts/office/soffice.py)


This skill is created and maintained by Anthropic. Vendored here unmodified except for frontmatter metadata; see LICENSE.txt for terms.

Individual skills in this repo

This repo contains 20 individual skills — each has its own dedicated page.

adaptyv

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aeon

This skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection, segmentation, and similarity search. Use when working with temporal data, sequential patterns, or time-indexed observations requiring specialized algorithms beyond standard ML approaches. Particularly suited for univariate and multivariate time series analysis with scikit-learn compatible APIs.

alphagenome

Look up precomputed AlphaGenome Atlas effects for any GRCh38 single-nucleotide variant (AVI score with Phred and 18 SHAP feature attributions, plus raw and quantile scores for RNA-seq, DNase, ATAC, ChIP-TF, ChIP-histone, CAGE, PRO-cap, splicing, polyadenylation and contact-map tracks), score variants or scan windows on demand with the AlphaGenome model for human and mouse (variant scoring, in silico mutagenesis, REF-versus-ALT track prediction), and build Atlas website deep links. Use when the user mentions AlphaGenome, AlphaGenome Atlas, AVI or AlphaGenome Variant Impact, DeepMind variant effect prediction, or wants to prioritise or mechanistically interpret non-coding, regulatory, splicing, enhancer, promoter, or chromatin-accessibility effects of SNVs from a VCF, credible set, or region. Research use only; not a clinical tool.

analytical-method-validation

Plan, execute, and document validation, verification, and transfer of analytical procedures under the governing framework - ICH Q2(R2) and Q14, USP <1220>/<1225>/<1226>, ICH M10 bioanalytical, CLSI EP, or ISO/IEC 17025. Use for HPLC, LC-MS/MS, GC, CE, ICP-MS, dissolution, qNMR, qPCR, NIR, and ligand binding or cell-based assays whenever the question is whether a procedure is fit for its intended purpose. Triggers include

anndata

Data structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem. This is the data format skill—for analysis workflows use scanpy; for probabilistic models use scvi-tools; for population-scale queries use cellxgene-census.

arbor

Autonomously improve a real artifact (code, training recipe, agent harness, data pipeline, prompt) against an objective and an evaluator, using Hypothesis Tree Refinement (HTR) from the Arbor paper. Use this whenever someone wants to iteratively optimize something over many experiments without overfitting — e.g.

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.

astropy

Core Python library for astronomy and astrophysics workflows that need Astropy APIs, including units/quantities, coordinates, FITS I/O, tables, time systems, WCS, and cosmology. Use when implementing or debugging astronomical data analysis code with Astropy.

autoskill

Observe the user

benchling-integration

Benchling Python SDK and REST API integration for registry entities, inventory, ELN entries, workflows, Benchling Apps, and Data Warehouse queries. Use when automating lab data with benchling-sdk or the v2 API.

bgpt-paper-search

Search scientific papers and retrieve structured experimental data extracted from full-text studies via the BGPT MCP server. Returns 25+ fields per paper including methods, results, sample sizes, quality scores, and conclusions. Use for literature reviews, evidence synthesis, and finding experimental details not available in abstracts alone.

bids

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biopython

Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices.

bioservices

Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID mapping across services. For quick single-database lookups use gget; for sequence/file manipulation use biopython.

bulk-rnaseq

End-to-end bulk RNA-seq orchestrator — takes raw FASTQ reads through QC and trimming (FastQC, fastp/Trim Galore), alignment and quantification (STAR, Salmon, featureCounts), assembles a gene-level counts matrix, then hands off to differential expression (pydeseq2), pathway/GSEA enrichment (pathway-enrichment), and publication figures (scientific-visualization). Use whenever the user has bulk RNA-seq reads or quant output and wants a complete, reproducible differential-expression workflow — e.g.

cellxgene-census

Query the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data. Use when you need population-scale cell metadata, gene expression slices, Census summary counts, source H5AD URIs/downloads, embeddings, spatial Census data, or reference atlas comparisons across organisms, tissues, diseases, assays, and cell types. For analyzing your own local single-cell data use scanpy, anndata, or scvi-tools.

cirq

Google quantum computing framework. Use when targeting Google Quantum AI hardware, designing noise-aware circuits, or running quantum characterization experiments. Best for Google hardware, noise modeling, and low-level circuit design. For IBM hardware use qiskit; for quantum ML with autodiff use pennylane; for physics simulations use qutip.

citation-management

Comprehensive citation management for academic research. Search OpenAlex, PubMed, and Google Scholar for papers, extract accurate metadata, validate citations, and generate properly formatted BibTeX entries. This skill should be used when you need to find papers, verify citation information, convert DOIs to BibTeX, or ensure reference accuracy in scientific writing.

clinical-decision-support

Prepare and validate research-only clinical decision-support evaluation, evidence-profile, cohort, survival, biomarker/model, privacy, and governance artifacts. Use for aggregate or synthetic research documentation and traceability—not patient care or live clinical operation.

clinical-reports

Create safety-bounded draft structures and run local deterministic checks for clinical case, diagnostic, trial, safety, and aggregate research reports. Use only with synthetic, de-identified, or aggregate inputs and verified source-fact manifests; every output requires qualified review.

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