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Claude Skills by BioTender-max
github.com/BioTender-max897 skills8 installs817 views
- PheeQuery the PHEE pharmacovigilance event extraction dataset. Use whenever the user asks about annotated adverse drug events, pharmacovigilance case reports, drug–effect associations from medical literature, or wants to find PHEE examples mentioning a drug name, adverse effect, or condition.Votes: 0GitHub stars: 171
- PsytarQuery the PsyTAR psychiatric adverse-reaction corpus. Use when the user asks about patient-reported ADRs, withdrawal symptoms, drug indications, or effectiveness for Zoloft, Lexapro, Cymbalta, or Effexor XR. Accepts drug names (brand or generic), symptom terms, or UMLS CUIs.Votes: 0GitHub stars: 171
- RepodbQuery the RepoDB drug repurposing database. Use whenever the user asks about drug-disease associations, drug repurposing candidates, or wants to look up any entity (drug name, indication, DrugBank ID, UMLS CUI, NCT ID) in RepoDB.Votes: 0GitHub stars: 171
- RepurposedrugsQuery the RepurposeDrugs single-agent drug repurposing database. Use whenever the user asks about drug-disease repurposing associations, clinical trial phases for repurposed drugs, or wants to look up any entity (drug name, disease name, NCT ID) in RepurposeDrugs.Votes: 0GitHub stars: 171
- Repurposing HubQuery the Broad Institute Drug Repurposing Hub (~6,800 compounds). Look up drugs by name, gene target, MOA, disease area, Broad ID, or InChIKey. Returns clinical phase, mechanism of action, targets, disease area, indication, and chemical identifiers.Votes: 0GitHub stars: 171
- RxnormQuery the RxNorm drug naming and normalization API. Use whenever the user asks to look up an RxCUI, normalize a drug name, find drug interactions, retrieve brand/trade names, or resolve any clinical drug name via RxNorm. Supports single drug or batch queries. Trigger on mentions of RxNorm, RxCUI, drug normalization, drug interaction lookup, or brand-name resolution.Votes: 0GitHub stars: 171
- Sematyp> Drug-Disease Association Knowledge Graph from literature mining + TTD > **Category:** Drug-centric | **Type:** KG | **Subcategory:** Drug-Disease Associations > **Access:** Local files (downloaded from GitHub) | Resource | URL | |----------|-----| | GitHub | https://github.com/ShengtianSang/SemaTyP | | Paper | https://link.springer.com/article/10.1186/s12859-018-2167-5 | ---Votes: 0GitHub stars: 171
- Sider**Category:** Drug-centric | **Type:** DB | **Subcategory:** Adverse Drug Reaction (ADR) **Link:** http://sideeffects.embl.de/ | **Paper:** https://doi.org/10.1093/nar/gkv1075 SIDER contains marketed medicines and their recorded adverse drug reactions, mined from public documents and package inserts.Votes: 0GitHub stars: 171
- StitchQuery the STITCH chemical-protein interaction database. Use whenever the user asks about chemical-protein interactions, drug-target binding, compound action modes, or wants to look up any entity (chemical name, STITCH CID, STRING protein ID) in STITCH.Votes: 0GitHub stars: 171
- Tac2017Query TAC 2017 ADR annotated drug labels for adverse drug reactions. Use whenever the user asks about ADRs extracted from FDA drug labels, MedDRA-normalized adverse reactions, or wants to look up a drug name, ADR string, or MedDRA code in the TAC 2017 ADR corpus.Votes: 0GitHub stars: 171
- TarkgQuery canonical TarKG drug-target triplets. Use when the user asks about drug-target interactions, relation labels, disease/pathway context, or quick lookups for drugs/targets in TarKG.Votes: 0GitHub stars: 171
- TtdQuery the Therapeutic Target Database (TTD) for drug-target-disease interaction data. Use this skill when the user asks about therapeutic targets, drugs, diseases, or their relationships — including target-drug mappings, clinical status of drugs, disease indications, UniProt/gene associations, and pathway annotations. Triggers on queries like "what drugs target EGFR", "which diseases is Imatinib used for", "find targets for lung cancer", or any lookup involving TTD IDs, gene symbols, drug nam...Votes: 0GitHub stars: 171
- Unid3UniD3 is a multi-knowledge-graph built from 150,000+ PubMed articles, stored as 6 GraphML files. It supports drug-disease matching, effectiveness assessment, and drug-target analysis.Votes: 0GitHub stars: 171
- UnitoxQuery the UniTox drug toxicity database. Use whenever the user asks about organ-system toxicity ratings for a drug, multi-organ toxicity profiles, or wants to look up any entity (drug name, SMILES, SPL_ID) in UniTox.Votes: 0GitHub stars: 171
- WebmdQuery the WebMD Drug Reviews dataset (~362 k patient reviews, 2007–2020). Use whenever the user asks about patient-reported drug effectiveness, ease of use, satisfaction ratings, side effects, or reviews for a specific drug or medical condition.Votes: 0GitHub stars: 171
- Who EmlQuery the WHO Model List of Essential Medicines (23rd list, 2023). Use whenever the user asks about essential medicines, WHO-recommended drugs, dosage forms, therapeutic sections, or AWaRe antibiotic classification.Votes: 0GitHub stars: 171
- Academic SlidesUse this skill for creating or refining an academic slide deck and the talk built around it: structuring a conference talk, thesis defense, lab meeting, or paper-to-slides deck; deciding the narrative arc and slide breakdown; improving slide design and visual hierarchy; planning rehearsal, timing, Q&A, and backup slides; or generating the .pptx. Reach for it when the user is shaping the presentation itself. Do not use for writing the paper, producing standalone speaker notes/scripts/transcrip...Votes: 0GitHub stars: 171
- Evo MemoryManages persistent research memory across ideation and experimentation cycles. Maintains two stores: Ideation Memory M_I (feasible/unsuccessful directions) and Experimentation Memory M_E (reusable strategies for data processing, model training, architecture, debugging). Three evolution mechanisms: IDE (after research-ideation), IVE (after experiment failure — classifies failures as implementation vs fundamental), ESE (after experiment success — extracts reusable strategies). Use when: updatin...Votes: 0GitHub stars: 171
- Evomath TaoUse this skill whenever the user submits a non-trivial mathematical claim that needs a rigorous proof or audit. Trigger on IMO/Putnam/USAMO/Olympiad-style problems, ML/AI theoretical statements, research conjectures, suspected-false claims, multi-step proofs the user already failed on, proof drafts with possible hidden assumptions, or any request containing 'prove rigorously', 'verify this', 'is this true', 'find the gap', 'audit my proof', 'find a counterexample', or 'use EvoMath' that targe...Votes: 0GitHub stars: 171
- Experiment CraftUse this skill when the user wants to debug, diagnose, or systematically iterate on an experiment that already exists, or when they need a structured experiment log for tracking runs, hypotheses, failures, results, and next steps during active research. Apply it to underperforming methods, training that will not converge, regressions after a change, inconsistent results across datasets, aimless experimentation without progress, and questions like 'why doesn't this work?', 'no progress after m...Votes: 0GitHub stars: 171
- Experiment Iterative CoderIterative code refinement through plan → code → evaluate → refine cycles. Runs lint checks (ruff), tests (pytest), and structured self-evaluation each cycle, then diagnoses failures and refines. Decomposes complex tasks into sequential phases, iterates up to 3 times per phase (10 total). Use when: the main agent delegates a code task with 'MODE: MORE_EFFORT', the user selects 'More Effort' code generation mode, or the task explicitly requests iterative refinement for higher code quality. Do N...Votes: 0GitHub stars: 171
- Experiment PipelineGuides structured 4-stage experiment execution with attempt budgets and gate conditions: Stage 1 initial implementation (reproduce baseline), Stage 2 hyperparameter tuning, Stage 3 proposed method validation, Stage 4 ablation study. Integrates with evo-memory (load prior strategies, trigger IVE/ESE) and experiment-craft (5-step diagnostic on failure). Use when: user has a planned experiment, needs to reproduce baselines, organize experiment workflow, or systematically validate a method. Do NO...Votes: 0GitHub stars: 171
- Nano BananaGenerate professional presentation slides and high-quality illustrations using Gemini image generation API (Nano Banana 2), with interactive browser-based review and iterative editing. Full workflow: content planning conversation → slides_plan.json → batch image generation → review with feedback → targeted slide editing → PPTX packaging. Use when: user wants to create a presentation, make slides, generate a PPT/PPTX, prepare a talk deck, design visual slide content, or generate high-quality f...Votes: 0GitHub stars: 171
- Paper NavigatorFind, read, download, and locally cache academic papers. Disambiguate ambiguous queries, discover via keyword search / citation traversal / recommendations / arXiv monitoring / trending / GitHub search, evaluate (TLDR, citations, code, SOTA), read using a 3-level strategy, and save PDFs to a local library for offline reuse. Use when finding a specific paper, listing papers on a topic, tracking recent advances, finding a baseline with code, reading or downloading a paper by URL, searching the ...Votes: 0GitHub stars: 171
- Paper PlanningGuides pre-writing planning for academic papers with 4 structured steps: story design (task-challenge-insight-contribution-advantage), experiment planning (comparisons + ablations), figure design (pipeline + teaser), and 4-week timeline management. Includes counterintuitive planning tactics (write a mock rejection letter to identify weaknesses before writing, narrow before broad claims, design ablations first). Use when: user wants to plan a paper before writing, design story/contributions, p...Votes: 0GitHub stars: 171
- Paper RebuttalGuides writing effective rebuttals after receiving peer review feedback. Covers review diagnosis (score-driven color-coding), response strategy (champion identification, common-theme consolidation), tactical writing (18 rules), and counterintuitive rebuttal principles. Use when: user received reviewer scores/comments, needs to write a rebuttal or author response, wants to respond to specific criticism (e.g. 'limited novelty', 'missing baselines'), mentions 'rebuttal', 'reviewer comments', 'au...Votes: 0GitHub stars: 171
- Paper ReviewGuides self-review of YOUR OWN academic paper before submission with adversarial stress-testing. Core method: 5-aspect checklist (contribution sufficiency, writing clarity, results quality, testing completeness, method design), counterintuitive protocol (reject-first simulation, delete unsupported claims, score trust, promote limitations, attack novelty), reverse-outlining, and figure/table quality checks. Use when: user wants to self-review or self-check their own paper draft before submissi...Votes: 0GitHub stars: 171
- Research IdeationEnd-to-end research ideation pipeline: literature grounding → multi-track idea generation (3 personas: innovator/pragmatist/critic) → iterative refinement → ELO tournament ranking → update evo-memory (IDE) → user selects direction → expand into manuscript-quality proposal. Use when: user wants to find a research direction, brainstorm ideas, evaluate idea novelty, design a novel solution, rank/compare research ideas, or generate a research proposal. Do NOT use for finding/searching/reading pap...Votes: 0GitHub stars: 171
- Research SurveyGenerates structured literature survey reports from collected papers using a multi-stage pipeline: outline generation (query-type adaptive) → draft survey → section-by-section expansion → summary section refinement → final assembly. Produces survey-grade output with taxonomy-based method analysis, LaTeX formalizations, comparative tables, and dense citations. Use when: user wants a literature review, research survey, field overview, or systematic synthesis of multiple papers. Do NOT use for f...Votes: 0GitHub stars: 171
- Exa SearchWeb toolkit powered by Exa, tuned for scientific and technical content. Use this skill when the user needs to search the web or fetch/extract URL content. Covers: web search (semantic lookups, research, current info — with optional research-paper category and academic domain filtering) and URL extraction (fetching pages, articles, academic PDFs in batch). Use this skill for web-related tasks when the user wants high-quality search or scholarly filtering via category=research paper. Triggers o...Votes: 0GitHub stars: 171
- PacsomaticOperator toolkit for nf-core/pacsomatic matched tumor-normal workflows from BAM inputs. Use this skill when the user needs to validate run inputs, generate pacsomatic-compliant samplesheets, prepare reproducible Nextflow launch artifacts, run locally or submit to schedulers (LSF/Slurm/PBS/SGE), and triage execution failures. Triggers on requests to run pacsomatic, prepare launch commands/scripts, perform dry-run checks, or troubleshoot pipeline startup and scheduler submission errors.Votes: 0GitHub stars: 171
- Academic Literature SearchUse this skill when the user asks to search for academic papers, retrieve literature, generate citations, format references, or any task involving PubMed, bioRxiv, arXiv, or academic reference management. Trigger keywords: "搜文献", "检索", "找论文", "参考文献", "引用", "citation", "search papers", "PubMed", "bioRxiv", "arXiv", "GB/T 7714", "PMID", "DOI", "批量引用".Votes: 0GitHub stars: 171
- Analyze Lab Video Cell BehaviorAutomated cell behavior analysis from microscopy or XR lab recordings. Classifies cell motion phenotypes (migration, proliferation, apoptosis, division, quiescence), computes population-level quantitative metrics (growth rate, migration velocity, directionality index), and emits structured JSON for downstream reporting, plotting, or ELN integration.Votes: 0GitHub stars: 171
- BioinformaticsComputational biology and genomics analysis pipelines. GENERAL: not locked to any specific tool — use Scanpy, Seurat, DESeq2, or any appropriate package.Votes: 0GitHub stars: 171
- ChemistryComputational chemistry, cheminformatics, and drug discovery workflows.Votes: 0GitHub stars: 171
- ClinicalClinical study design, statistical analysis, and regulatory compliance for medical research.Votes: 0GitHub stars: 171
- Detect Common Wetlab ErrorsDetects common wet-lab procedural and safety errors from XR or fixed-camera lab video. Identifies pipette volume deviations, forgotten reagent additions, uncapped tubes, contamination risks, sample mix-ups, and other observable hazards. Outputs structured JSON with error type, timestamp, severity, and corrective action suggestions for real-time alerts or post-hoc audit.Votes: 0GitHub stars: 171
- Egocentric View To Structured LogConverts first-person XR headset video into a structured experiment timeline log. Extracts timestamped events (action, object, location, result) via VLM or action recognition, outputs Markdown or JSON for downstream analysis, reporting, protocol compliance audit, or ELN attachment.Votes: 0GitHub stars: 171
- Egohos SegmentationEgocentric Hand-Object Segmentation (EgoHOS) - pixel-level hand and object segmentation in egocentric videos. Outputs fine-grained segmentation masks with hand regions highlighted. Specialized for hand-object interaction scenarios with pixel-accurate masks. Ideal for detailed interaction analysis.Votes: 0GitHub stars: 171
- Export Experiment Data To ExcelExports any structured experimental data (JSON, tables, time series) to well-formatted Excel (.xlsx) files. Auto-names sheets (Raw Data, Growth Curves, Cell Counts, etc.), adds unit headers and annotation rows, applies consistent styling, and produces lab-ready spreadsheets for sharing, archival, or downstream analysis in R, pandas, or Excel.Votes: 0GitHub stars: 171
- Extract Experiment Data From VideoGeneral-purpose experimental data extractor from lab video streams. Ingests footage from XR headsets or fixed cameras and extracts typed, timestamped measurements — liquid volume levels, color/turbidity shifts, cell and colony counts, pipette readouts, instrument display values, gel band intensities — emitting a time-series JSON or CSV table ready for downstream analysis, charting, or ELN attachment.Votes: 0GitHub stars: 171
- Fair DataGuidelines for making scientific data FAIR: Findable, Accessible, Interoperable, and Reusable.Votes: 0GitHub stars: 171
- Gaussian Splatting Scene DescriptionGenerates natural language scene descriptions from 3D Gaussian Splatting reconstructions built from lab photos or short video clips. Outputs structured text with instrument placement, sample positions, spatial layout keywords, and relational predicates — optimized for VLM or spatial intelligence model consumption in protocol guidance, error detection, or AR overlay generation.Votes: 0GitHub stars: 171
- Generate Cell Analysis ChartsDomain-specialized chart generator for cell biology video analysis outputs. Consumes structured JSON from analyze_lab_video_cell_behavior or compatible sources and produces publication-ready figures — growth curves, cell trajectory maps, phenotype distribution charts, MSD plots, wound-closure timeseries, dose-response curves, and 96-well heatmaps — using matplotlib and seaborn. Exports PNG/PDF at configurable DPI for papers, ELN entries, or XR dashboards.Votes: 0GitHub stars: 171
- Generate Double Column Pdf ReportAssembles experimental data, figures, methods, and results into a journal-style double-column PDF report. Uses reportlab or PyMuPDF for programmatic generation with title page, embedded figures/tables, section headings, body text flow, and reference placeholders — suitable for internal lab reports, preprint drafts, or journal submission-ready layouts.Votes: 0GitHub stars: 171
- Generate Scientific Method SectionAutomated SCI-standard Methods section generator from experiment execution records. Parses LabOS skill call chains, structured JSON logs (extract_experiment_data_from_video, analyze_lab_video_cell_behavior), protocol text, and ELN entries to produce flowing, past-tense, passive-voice Methods prose with full reagent citations, equipment model numbers, and statistical analysis subsections. Outputs LaTeX (\subsection{} / \paragraph{}) or Markdown, ready for direct insertion into a manuscript draft.Votes: 0GitHub stars: 171
- Hand Tracking ToolkitFacebook Research Hand Tracking Challenge Toolkit - evaluation and visualization tools for 3D hand tracking. Supports loading HOT3D data, computing metrics (PA-MPJPE, AUC, etc.), visualizing 3D pose projections, and generating tracking evaluation reports. Essential for benchmarking hand tracking algorithms.Votes: 0GitHub stars: 171
- Hands 3d PoseHigh-quality 3D hand pose estimation for egocentric videos from ECCV 2024 (ap229997/hands). Provides 3D joint keypoints and skeleton visualization projected to 2D. Optimized for daily egocentric activities with state-of-the-art accuracy. Outputs hand skeleton overlays on video frames.Votes: 0GitHub stars: 171
- HandtrackingReal-time hand detection in egocentric videos using victordibia/handtracking. Outputs bounding boxes for hands, specifically trained on EgoHands dataset. Supports video input/output with labeled hand boxes. Lightweight and fast for egocentric view applications.Votes: 0GitHub stars: 171
- Hot3dHOT3D (Hand-Object 3D Dataset) by Meta Facebook - multi-view egocentric hand and object 3D tracking for Aria/Quest smart glasses. State-of-the-art multi-view 3D hand pose, object pose, and hand-object interaction tracking. Supports visualization with 3D joint projections, meshes, and skeletal overlays on video frames.Votes: 0GitHub stars: 171