Docs & Writing

fridrichmethod Bundle

Interact with Zotero reference management libraries using the pyzotero Python client. Retrieve, create, update, and delete items, collections, tags, and attachments via the Zotero Web API v3. Use this skill when working with Zotero libraries programmatically, managing bibliographic references, exporting citations, searching library contents, uploading PDF attachments, or building research automation workflows that integrate with Zotero.

fridrichmethod Bundle

Low-level plotting library for full customization. Use when you need fine-grained control over every plot element, creating novel plot types, or integrating with specific scientific workflows. Export to PNG/PDF/SVG for publication. For quick statistical plots use seaborn; for interactive plots use plotly; for publication-ready multi-panel figures with journal styling, use scientific-visualization.

fridrichmethod Bundle

Search 11 academic literature APIs for papers, preprints, citations, and open-access full text, and return results with reproducible provenance. Covers PubMed, PMC (full text), Europe PMC (full-text and preprint search), bioRxiv, medRxiv, arXiv, OpenAlex, Crossref, Semantic Scholar, CORE, Unpaywall. Use when searching for papers, citations, DOI/PMID/arXiv lookups, abstracts, full text, open-access PDFs, preprints, citation graphs, author publications, or any scholarly literature query. Triggers on mentions of any supported database or requests like "find papers on X", "look up this DOI", "who cites this paper", or "get me the PDF".

fridrichmethod Bundle

Quality control for IMC/MIBI data across pixel, channel, image, slide, and batch levels, covering Poisson-count SNR (cell-level Gaussian-mixture and empty-channel comparison), spillover-matrix QC (the three physical sources), drift and the missing EQ-bead analog, acquisition artifacts, and sample-of-origin batch effects. Use when deciding whether to keep or drop a channel, ROI, or slide, distinguishing a dim antibody from a failed one, reading a spillover matrix, or diagnosing batch-driven clustering before analysis.

zaxbysauce Bundle

Use when asked to trace, investigate, root-cause, reproduce, plan, fix, resolve, close, or prepare a PR for an issue, bug report, defect, regression, failing test, or confusing runtime behavior. This Codex adapter delegates to the canonical protocol at .opencode, which owns the Full-Resolution Contract, reproduction, reasoning-guided localization, no-gap fix planning, recurrence-class eradication, independent critic and implementation review, and PR-ready closure.

zaxbysauce Skill

Use when asked to trace, investigate, root-cause, reproduce, plan, fix, resolve, close, or prepare a PR for an issue, bug report, defect, regression, failing test, or confusing runtime behavior. This Claude Code adapter delegates to the canonical protocol at .opencode, which owns the Full-Resolution Contract, reproduction, reasoning-guided localization, no-gap fix planning, recurrence-class eradication, independent critic and implementation review, and PR-ready closure.

zaxbysauce Skill

Apply when planning fixes, investigating tech debt, architecting solutions, or diagnosing unknown issues that may involve external frameworks, dependencies, or platform behavior. Search online for current documentation and state-of-the-art approaches before tracing through code.

zaxbysauce Bundle

Evidence-first investigation, validation, and full resolution of issues and bugs. Use when asked to investigate, trace, root-cause, reproduce, plan, fix, resolve, close, or prepare a PR for an issue, bug report, defect, regression, failing test, crash, or confusing runtime behavior. Drives issue validation, acceptance-check-driven reproduction and fix planning, independent critic and implementation review, recurrence-class eradication, and an invariant-aware, PR-ready closure with a recorded human merge gate under a mandatory full-resolution contract that forbids partial fixes, deferred work, and unwired code.

onyx-dot-app Bundle

Use this skill any time a .pptx file is involved in any way — as input, output, or both. This includes: creating slide decks, pitch decks, or presentations; reading, parsing, or extracting text from any .pptx file (even if the extracted content will be used elsewhere, like in an email or summary); editing, modifying, or updating existing presentations; combining or splitting slide files; working with templates, layouts, speaker notes, or comments. Trigger whenever the user mentions "deck," "slides," "presentation," or references a .pptx filename, regardless of what they plan to do with the content afterward. If a .pptx file needs to be opened, created, or touched, use this skill.

francostino Bundle

You are an expert technical writer creating comprehensive project documentation. Your goal is to write a README.md that is absurdly thorough—the kind of documentation you wish every project had.

francostino Skill

Review MDPR Markdown presentation workflows with semantic hints, visual checks, and deterministic renderer boundaries.

francostino Bundle

Go in depth harness — fan-out web searches, fetch sources, adversarially verify claims, synthesize a cited report.

francostino Bundle

Scrapes content based on a preset URL list, filters high-quality technical information, and generates daily Markdown reports.

fridrichmethod Bundle

Detects contamination in sequencing reads - cross-species (FastQ Screen, Kraken2), vector/PhiX/adapter, rRNA, and same-species cross-sample/index-hopping and sample swaps (SNP fingerprints via verifyBamID2/NGSCheckMate/somalier). Use when suspecting cross-contamination, PDX host reads, microbial carry-over, or sample swaps, and to decide whether to report, filter, or align to a combined reference. For deep taxonomic profiling use metagenomics/kraken-classification.

fridrichmethod Bundle

Reconstructs single cells from sub-cellular spatial capture units (Visium HD 2um bins, Stereo-seq DNB spots, Slide-seqV2 beads) by aggregating bins UP into cells rather than deconvolving a mixture DOWN. Use when choosing a bin size and recognizing the sparsity-vs-mixture dilemma (2um bins are too sparse to cluster, but binning to 8/16um re-creates the multi-cell mixture deconvolution was meant to escape); deciding between morphology-driven cell reconstruction (Bin2cell -- StarDist/Cellpose nuclei on a registered H&E/DAPI image, then assign 2um bins to nuclei) and fixed-bin aggregation by whether a co-registered cell image exists; recognizing this as the INVERSE of deconvolution (bin UP, not mix DOWN -- this is the AMBIGUOUS regime of the resolution fork); and handling each platform (Visium HD has an image so reconstruct, Slide-seqV2 has no per-bead image so aggregate or deconvolve, Stereo-seq depends on a registered stain).

fridrichmethod Bundle

Build evidence-traceable market research reports and assumption-driven market sizing or forecast scenarios. Use for market definition, industry and customer evidence, competitive landscapes, TAM/SAM/SOM reconciliation, forecast sensitivity, and auditable report scaffolds.

jeremylongshore Skill

Analyze and explain TimeGPT forecast results in plain English. Generates executive summaries with driver analysis. Use when stakeholders need forecast explanations, board presentations, or compliance documentation. Trigger with "explain forecast", "why is the forecast", "forecast narrative".

caixinyu2017-star Bundle

制作精美 PPT。当用户需要为论文、项目、竞赛、答辩、汇报、路演做幻灯片时使用。设计封面/目录/过渡/内容/图表/流程/时间线/对比/团队/结论/致谢等页。逻辑清晰、排版高级、审美统一、重点突出，按主题选风格（学术/科技/农业/医学/商务/极简/浅色/深色/数据可视化/竞赛路演）。不仅生成内容，还规划整套叙事逻辑、视觉风格、页面层次与演讲节奏。

caixinyu2017-star Bundle

根据目标期刊/会议/学校/比赛要求做 LaTeX 或 Word 排版并编译导出最终 PDF/Word。当用户需要套模板、排版、解决编译错误、导出论文时使用。处理标题层级、页边距、目录、摘要、关键词、公式、图表、算法伪代码、参考文献、附录、页眉页脚、页码、单/双栏、编号、交叉引用，并检查 LaTeX 编译错误、Word 格式问题、引用错误、图片位置、字体一致性、编号混乱。

caixinyu2017-star Bundle

从顶会大牛角度进行专业绘图与组图。当用户需要把规划好的图实际画出来时使用。按情况用 Python(matplotlib/seaborn/plotly/altair)、R(ggplot2)、MATLAB、Visio、Origin、LaTeX/TikZ、Illustrator、PowerPoint 等。审美统一、专业清晰、配色合理、字体规范、线条清楚、高分辨率，适合直接投稿。不仅画图，还从论文表达角度判断怎么排、怎么组、怎么标注、怎么突出重点。

caixinyu2017-star Bundle

Multi-perspective academic paper review with dynamic reviewer personas. Simulates 5 independent reviewers (EIC + 3 peer reviewers + Devil's Advocate) with field-specific expertise. Supports full review, re-review (verification), quick assessment, methodology focus, Socratic guided, and calibration modes. Triggers on: review paper, peer review, manuscript review, referee report, review my paper, critique paper, simulate review, editorial review, calibrate reviewer, reviewer calibration, measure reviewer accuracy.

caixinyu2017-star Bundle

Marp Slides 制作助手

caixinyu2017-star Skill

Generate conference presentation slides (beamer LaTeX → PDF + editable PPTX) from a compiled paper, with speaker notes and full talk script. Use when user says "做PPT", "做幻灯片", "make slides", "conference talk", "presentation slides", "生成slides", "写演讲稿", or wants beamer slides for a conference talk.

fridrichmethod Bundle

Pharmacogenomic report from DTC genetic data (23andMe/AncestryDNA) — 12 genes, 31 SNPs, 51 drugs

fridrichmethod Bundle

Scientific presentations for conferences, seminars, thesis defenses, and grant pitches. Slide design, talk structure, timing, data viz for slides, QA. PowerPoint and LaTeX Beamer. For posters use latex-research-posters.

fridrichmethod Bundle

Designs and validates quantitative targeted metabolomics assays (MRM/SRM on triple-quadrupole, PRM on high-resolution instruments) to report absolute concentrations. Covers the internal-standard strategy (external cal -> global IS -> standard addition -> stable-isotope-labeled IS), weighted calibration judged by back-calculated %RE not R-squared, ion-ratio quantifier/qualifier confirmation, matrix-effect/recovery characterization, and ICH M10 method validation. Use when quantifying a closed panel of known metabolites with units, building or validating an LC-MS/MS assay, choosing an IS or calibration weighting, or judging whether a reported concentration is trustworthy. For untargeted feature detection see metabolomics/xcms-preprocessing; for group statistics see metabolomics/statistical-analysis; for flux/MID/tracing see metabolomics/isotope-tracing.

fridrichmethod Bundle

Checks whether a PCR primer PAIR amplifies only the intended target genome-wide, using pair-aware in-silico PCR (MFEprimer-3.0, UCSC isPcr, NCBI Primer-BLAST) plus a primer3-py 3'-end-stability prefilter, against the correct database. Covers why plain BLAST is the wrong tool (it scores per-primer similarity, blind to 3'-terminal anchoring and to whether the two primers form a convergent amplicon in range), why a single 3'-terminal mismatch suppresses amplification while internal mismatches are tolerated, why intron-spanning RT-qPCR is defeated by processed pseudogenes that force a GENOME search not transcriptome-only, how to read a Primer-BLAST report (empty unintended-products means none passed its filter, not none exist), and that in-silico checking reduces but never replaces empirical validation. Use when confirming specificity, screening off-target amplicons, avoiding paralog/pseudogene hits, or checking SNPs under the 3' end. Design is primer-basics; dimers primer-validation; alignment read-alignment.

fridrichmethod Skill

Selecting a reference manager and applying citation styles. Compares Zotero, Mendeley, EndNote, Paperpile; covers APA/Vancouver/ACS/Nature styles, DOI management, citation tracking, and Word/Google Docs/LaTeX integration. Use when setting up a reference workflow or fixing citation formatting.

fridrichmethod Bundle

Extracts per-cytosine methylation calls from aligned bisulfite/EM-seq reads with bismark_methylation_extractor (Bismark BAM) or the aligner-agnostic MethylDackel/BISCUIT (bwa-meth BAM), producing the beta value M/(M+U) as a coverage file, bedGraph, or genome-wide cytosine report across CpG/CHG/CHH context. Covers conversion-rate QC as the first gate, the 5mC vs 5hmC summed caveat, variant-aware calling so a C/T SNP does not masquerade as unmethylation, paired-end --no_overlap double-counting, symmetric CpG dyad collapse, and the 0-based vs 1-based coordinate trap. Use when extracting methylation levels from a bisulfite/EM-seq alignment, choosing an extractor for a non-Bismark BAM, QC-ing conversion efficiency, or producing coverage/cytosine-report input for testing. For long-read MM/ML modification calling see long-read-sequencing/nanopore-methylation; for the upstream BAM see bismark-alignment; for per-CpG statistics see differential-cpg-testing.

fridrichmethod Bundle

Turns shotgun classifier output into a defensible abundance table with Bracken Bayesian re-estimation, then compositional treatment (CLR, zero handling), library-size normalization, reference-frame differential abundance, and optional absolute quantification. Covers why a relative-abundance change is not a change, why Bracken read fractions and MetaPhlAn percentages are different physical quantities, the silent -r read-length bias, the genome-size confound no library-size method fixes, and the rarefaction debate. Use when estimating species abundance from a Kraken2 report, normalizing a community count table, choosing a compositional transform, or converting relative to absolute load. For classification see kraken-classification; for diversity/ordination/DA mechanics see metagenome-visualization.

fridrichmethod Bundle

Predicts community functional POTENTIAL from 16S/ITS amplicon ASVs with PICRUSt2 (or q2-picrust2) by phylogenetic interpolation of reference-genome gene content - EPA-ng placement, gappa, castor hidden-state prediction of KO/EC/Pfam copy number, 16S copy-number normalization, and MinPath MetaCyc/KEGG pathways - gated by the NSTI quality index. Covers why predicted function is taxonomy re-encoded (never measured gene content and never activity), the mandatory NSTI report (--max_nsti 2 silently drops novel ASVs), why accuracy IS reference coverage (gut Spearman ~0.8, soil/marine collapse), the circularity trap, and Tax4Fun2/FAPROTAX/BugBase alternatives. Use when inferring KO/EC/MetaCyc potential from an ASV table, gating on NSTI, or choosing a prediction method. For MEASURED shotgun function see metagenomics/functional-profiling; for enrichment of KO lists see pathway-analysis/go-enrichment; for DA of predicted tables see differential-abundance.

intense-visions Bundle

Design Documentation

aetherlight-ai Bundle

Bug Report Skill

aetherlight-ai Bundle

Bug Report Template Skill

moosegoose0701 Bundle

Use when the task involves reading, creating, or editing `.docx` documents, especially when formatting or layout fidelity matters; prefer `python-docx` plus the bundled `scripts/render_docx.py` for visual checks.

bosh-kuo Bundle

Use this skill whenever the user wants to do anything with PDF files. This includes reading or extracting text/tables from PDFs, combining or merging multiple PDFs into one, splitting PDFs apart, rotating pages, adding watermarks, creating new PDFs, filling PDF forms, encrypting/decrypting PDFs, extracting images, and OCR on scanned PDFs to make them searchable. If the user mentions a .pdf file or asks to produce one, use this skill.