BioTender-max
- 258 skills
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- 3 days ago last updated
- ▌ Fda Database · biotender-maxQuery openFDA REST API for adverse events (FAERS), labeling, product info, recalls, enforcement. Search by drug name, ingredient, MedDRA, or NDC. 1k req/day no key; 120k with free key. For trials use clinicaltrials-database-search; for structures use drugbank-database-access or chembl-database-bioactivity.
- ▌ Geo Database · biotender-maxNCBI GEO access via GEOparse and E-utilities. Search by keyword/organism/platform, download GSE series matrices, parse GPL annotations, extract GSM metadata, load expression matrices into pandas. For single-cell use cellxgene-census; for multi-DB access use gget-genomic-databases.
- ▌ Bio Flow Cytometry Fcs Handling · biotender-max bundleRead and manipulate Flow Cytometry Standard (FCS) files. Covers loading data, accessing parameters, and basic data exploration. Use when loading and inspecting flow or mass cytometry data before preprocessing.
- ▌ Bio Proteomics Ptm Analysis · biotender-max bundlePost-translational modification analysis including phosphorylation, acetylation, and ubiquitination. Covers site localization, motif analysis, and quantitative PTM analysis. Use when analyzing phosphoproteomic data or other modification-enriched samples.
- ▌ Bio Pdb Structure Io · biotender-max bundleParse and write protein structure files using Biopython Bio.PDB. Use when reading PDB, mmCIF, and MMTF files, downloading structures from RCSB PDB, or writing structures to various formats.
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- ▌ Pubmed Search · biotender-maxSearch PubMed for scientific literature. Use when the user asks to find papers, search literature, look up research, find publications, or asks about recent studies. Triggers on "pubmed", "papers", "literature", "publications", "research on", "studies about".
- ▌ Writing Plans · biotender-maxUse when you have a spec or requirements for a multi-step task, before touching code
- ▌ Bio Hi C Analysis Contact Pairs · biotender-max bundleProcess Hi-C read pairs using pairtools. Parse alignments, filter duplicates, classify pairs, and generate contact statistics from Hi-C sequencing data. Use when processing raw Hi-C read pairs.
- ▌ Bio Epidemiological Genomics Phylodynamics · biotender-max bundleConstruct time-scaled phylogenies and infer evolutionary dynamics using TreeTime and BEAST2 for outbreak analysis. Estimate divergence times, molecular clock rates, and ancestral states. Use when dating outbreak origins, estimating transmission rates, or building time-calibrated trees.
- ▌ Bio Hi C Analysis Tad Detection · biotender-max bundleCall topologically associating domains (TADs) from Hi-C data using insulation score, HiCExplorer, and other methods. Identify domain boundaries and hierarchical domain structure. Use when calling TADs from Hi-C insulation scores.
- ▌ Diffdock · biotender-max bundlePredict small-molecule binding poses with DiffDock-L (Corso et al. 2023/2024, github.com/gcorso/DiffDock) — blind diffusion docking that places a ligand into a protein pocket without a predefined search box and ranks the samples with a learned confidence model. Reach for this skill to dock a SMILES or SDF against a PDB, to generate ranked 3D poses for a small fragment library, or to get a starting pose for downstream rescoring. DiffDock predicts geometry, not affinity.
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- ▌ Uspto Database · biotender-maxAccess USPTO patent data via PatentsView REST API and Google Patents Public Data (BigQuery). Search by inventor, assignee, CPC, or keywords; download metadata and claims; analyze portfolios; track tech trends. For IP landscape analysis, competitor monitoring, prior art search, and tech forecasting in life sciences and biotech.
- ▌ Customize · biotender-maxCreate, configure, and maintain custom agent profiles and author new skills via the `repl` tool. Use when the user wants to create an agent profile, build a custom agent, modify agent capabilities, attach or detach skills/connectors on a profile, author a skill, or inspect which connectors and tools are available. Also use whenever you need the `host.agents.*` or `host.skills.*` Python SDK.
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- ▌ Grief Companion · biotender-max bundleCompassionate bereavement support, memorial creation, grief education, and healing journey guidance. Specializes in understanding grief stages, creating meaningful tributes, and supporting the non-linear path of loss.
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- ▌ Pubmed Database · biotender-max bundleProgrammatic PubMed access via NCBI E-utilities REST API. Covers Boolean/MeSH queries, field-tagged search, endpoints (ESearch, EFetch, ESummary, EPost, ELink), history server for batches, citation matching, systematic review strategies. Use for biomedical literature search or automated pipelines.
- ▌ Bio Single Cell Cell Annotation · biotender-max bundleAutomated cell type annotation using reference-based methods including CellTypist, scPred, SingleR, and Azimuth for consistent, reproducible cell labeling. Use when automatically annotating cell types using reference datasets.
- ▌ Bio Long Read Sequencing Isoseq Analysis · biotender-max bundleAnalyze PacBio Iso-Seq data for full-length isoform discovery and quantification. Use when characterizing transcript diversity or identifying novel splice variants.
- ▌ Bio Single Cell Lineage Tracing · biotender-max bundleReconstruct cell lineage trees from CRISPR barcode tracing or mitochondrial mutations. Use when studying clonal dynamics, cell fate decisions, or developmental trajectories.
- ▌ Bio Epidemiological Genomics Pathogen Typing · biotender-max bundlePerform multi-locus sequence typing (MLST), core genome MLST, and SNP-based strain typing for bacterial isolate characterization using mlst and chewBBACA. Use when identifying strain types, tracking outbreak clones, or characterizing bacterial isolates.
- ▌ Bio Imaging Mass Cytometry Quality Metrics · biotender-max bundleQuality metrics for IMC data including signal-to-noise, channel correlation, tissue integrity, and acquisition QC. Use when assessing data quality before analysis or troubleshooting problematic acquisitions.
- ▌ Bio Spatial Transcriptomics Spatial Data Io · biotender-max bundleLoad spatial transcriptomics data from Visium, Xenium, MERFISH, Slide-seq, and other platforms using Squidpy and SpatialData. Read Space Ranger outputs, convert formats, and access spatial coordinates. Use when loading Visium, Xenium, MERFISH, or other spatial data.
- ▌ Scvi Tools · biotender-max bundleProbabilistic single-cell RNA-seq with scvi-tools — scVI for a batch-corrected latent space, scANVI for semi-supervised label transfer, and Bayesian differential expression. Reach for this skill to integrate scRNA-seq batches, embed cells for clustering, transfer annotations from a reference onto a query, or score differentially expressed genes per cluster. For spatial deconvolution / mapping use the cell2location, DestVI, or Tangram methods instead.
- ▌ Claw Ancestry Pca · biotender-max bundleAncestry decomposition PCA against the Simons Genome Diversity Project
- ▌ Claw Metagenomics · biotender-max bundleShotgun metagenomics profiling — taxonomy, resistome, and functional pathways
- ▌ Pubmed Summariser · biotender-max bundleSearch PubMed for a gene name or disease term and generate a structured research briefing of the top recent English-language papers.
- ▌ Biomed Dispatch · biotender-maxDispatch biomedical research and data analysis tasks to Claude Code with K-Dense Scientific Skills. Use this skill when the user asks to run any bioinformatics, genomics, drug discovery, clinical data analysis, proteomics, multi-omics, medical imaging, or scientific computation task. Also use for literature search (PubMed, bioRxiv), pathway analysis, protein structure prediction, or scientific writing tasks.
- ▌ Paper Reproduce · biotender-maxSystematic methodology for reproducing published academic papers using provided data. Use when the user asks to reproduce, replicate, or verify results from a published paper, including sample selection, descriptive statistics, regression analyses, and generating reproduction reports (Markdown + LaTeX PDF). Covers the full pipeline: data exploration, variable identification/mapping, sample filtering, variable construction, statistical analysis, result comparison, and documentation. Applicable to any observational study, clinical cohort, or survey-based research paper.
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- ▌ Clinpgx Database · biotender-maxQuery the ClinPGx (formerly PharmGKB) REST API plus the CPIC PostgREST companion API for pharmacogenomic clinical annotations, CPIC/DPWG dosing guidelines, gene-drug pairs, variant-drug associations, FDA/EMA drug labels, and PGx pathways. Two-host architecture: api.clinpgx.org for annotation records, api.cpicpgx.org for genotype→recommendation lookups. No auth. For germline pathogenicity use clinvar-database; for somatic cancer PGx use cosmic-database or opentargets-database; for drug bioactivity use chembl-database-bioactivity.
- ▌ Bio Multi Omics Mofa Integration · biotender-max bundleMulti-Omics Factor Analysis (MOFA2) for unsupervised integration of multiple data modalities. Identifies shared and view-specific sources of variation. Use when integrating RNA-seq, proteomics, methylation, or other omics to discover latent factors driving biological variation across modalities.
- ▌ PDF Explore · biotender-max bundleUse this skill when the user has attached a PDF, paper, report, or other document and the answer needs content from more than one place in it: summarize the methods or any other section, compare sections, find where a topic is discussed, read a value or label off a figure or chart, or find/list/extract every instance of something across the whole document (datasets, benchmarks, citations, figures, table rows, accession numbers — including appendices). Skip it only for a single lookup of 1–4 pages quoted in your very next response — `read_file(pages=[...])` attaches pages as images that are dropped from context after one turn, so multi-section answers end up re-reading the same ranges repeatedly. Parses the PDF once in the Python kernel: `pdf_pages` (pages as persistent text), `pdf_outline` (TOC), `pdf_scan` (rank pages by relevance), `pdf_map`/`pdf_extract` (per-page summary / structured fields via parallel haiku calls). For PDF creation/manipulation, use reportlab/pypdf directly.
- ▌ Scrna Orchestrator · biotender-max bundleLocal Scanpy pipeline for single-cell RNA-seq QC, optional doublet detection, clustering, marker discovery, optional CellTypist annotation, optional latent downstream mode from integrated.h5ad/X_scvi, and optional dataset-level plus within-cluster contrastive marker analysis from raw-count .h5ad or 10x Matrix Market input.
- ▌ Variant Annotation · biotender-max bundleAnnotate VCF variants with Ensembl VEP REST, ClinVar significance, gnomAD/population frequency context, and prioritized variant ranking.
- ▌ Charls Reproduce · biotender-maxCHARLS (China Health and Retirement Longitudinal Study) database-specific knowledge for reproducing published papers. Use when reproducing or analyzing papers that use CHARLS data, including variable mapping from harmonized to raw questionnaire items, cognitive function scoring (episodic memory, mental status, TICS), CESD-10 depression screening, social isolation index construction, and chronic disease coding. Also use for any CHARLS data cleaning, variable construction, or cohort selection task.
- ▌ Feishu Rich Card · biotender-maxSend rich interactive cards with embedded images in Feishu group chats. Use when reporting progress, sharing analysis results, or presenting any content that benefits from mixed text+image layout in Feishu. Combines SVG UI templates (or matplotlib/PIL charts) with Feishu Card Kit API.
- ▌ Svg UI Templates · biotender-maxGenerate professional SVG UI panels for structured information display. Use when presenting lists, task checklists, pipeline/dependency status diagrams, or rich-text report layouts as SVG images. Covers four templates - list-panel, checklist-panel, pipeline-status, richtext-layout. Style is professional, business-oriented, academic-grade with Material Design color palette.
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- ▌ Literature Search · biotender-max bundleComprehensive scientific literature search across PubMed, arXiv, bioRxiv, medRxiv. Natural language queries powered by Valyu semantic search.
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- ▌ Astropy Astronomy · biotender-max bundleCore Python library for astronomy/astrophysics: units with dimensional analysis, celestial coordinate transforms (ICRS/Galactic/AltAz/FK5), FITS I/O, tables (FITS/HDF5/VOTable/CSV), cosmology (Planck18, distance/age), precise time (UTC/TAI/TT/TDB, Julian, barycentric), WCS pixel-world mapping, model fitting. For general tables use pandas/polars; for radio interferometry use CASA.
- ▌ Openalex Database · biotender-maxQuery OpenAlex REST API for 250M+ scholarly works, authors, institutions, journals, concepts. Search by keyword, author, DOI, ORCID, or ID; filter by year, OA, citations, field; retrieve citations, references, author disambiguation. Free, no auth. For PubMed use pubmed-database; preprints use biorxiv-database.
- ▌ Bio Imaging Mass Cytometry Cell Segmentation · biotender-max bundleCell segmentation from multiplexed tissue images. Covers deep learning (Cellpose, Mesmer) and classical approaches for nuclear and whole-cell segmentation. Use when extracting single-cell data from IMC or MIBI images after preprocessing.
- ▌ Bio Flow Cytometry Doublet Detection · biotender-max bundleDetect and remove doublets from flow and mass cytometry data. Covers FSC/SSC gating and computational doublet detection methods. Use when filtering out cell aggregates before clustering or quantitative analysis.
- ▌ Bio Hi C Analysis Hic Visualization · biotender-max bundleVisualize Hi-C contact matrices, TADs, loops, and genomic features using matplotlib, cooltools, and HiCExplorer. Create triangle plots, virtual 4C, and multi-track figures. Use when visualizing contact matrices or genomic features.
- ▌ Figure Style · biotender-max bundlePublication-grade figure correctness and legibility rules. Load before drawing any plot and call `apply_figure_style()` — sets a role-mapped font-size ladder, outward ticks, frameless legends, and 300-dpi output. The skill is a checklist, not a house look: data fidelity (claim-titles tested against every row, excluded data never enters summaries), label economy (floor and ceiling), colour threading, chart-choice-by-data-shape, layout, and a render-then-verify QA loop (bbox collision + per-panel perceptual check). Ships helpers: focal_palette, bar_with_points, strip_with_median, end_of_line_labels, panel_letter, set_frame, panel_crops. For multi-panel figures load `figure-composer`; for whole-paper figure arc load `paper-narrative`.
- ▌ Affinity Proteomics · biotender-max bundleUnified analysis pipeline for affinity-based proteomics platforms — Olink (PEA, NPX) and SomaLogic SomaScan (SOMAmer, RFU). Platform-aware QC, normalisation, differential abundance, volcano plots, heatmaps, and PCA.
- ▌ Bioconductor Bridge · biotender-max bundleBioconductor package discovery, workflow recommendation, setup inspection, and starter code generation grounded in official Bioconductor containers and BiocManager.
- ▌ Research Ideation · biotender-maxEnd-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 papers (use paper-navigator), literature survey reports (use research-survey), or planning a paper (use paper-planning).
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- ▌ Single Cell Rna Qc · biotender-max bundlePerforms quality control on single-cell RNA-seq data (.h5ad or .h5 files) using scverse best practices with MAD-based filtering and comprehensive visualizations. Use when users request QC analysis, filtering low-quality cells, assessing data quality, or following scverse/scanpy best practices for single-cell analysis.
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- ▌ Bio Imaging Mass Cytometry Data Preprocessing · biotender-max bundleLoad and preprocess imaging mass cytometry (IMC) and MIBI data. Covers MCD/TIFF handling, hot pixel removal, and image normalization. Use when starting IMC analysis from raw MCD files or preparing images for segmentation.
- ▌ Bio Proteomics Spectral Libraries · biotender-max bundleBuild, manage, and search spectral libraries for proteomics. Use when creating or working with spectral libraries for DIA analysis. Covers DDA-based library generation, predicted libraries (Prosit, DeepLC), and library formats.
- ▌ Bio Metabolomics Xcms Preprocessing · biotender-max bundleXCMS3 workflow for LC-MS/MS metabolomics preprocessing. Covers peak detection, retention time alignment, correspondence (grouping), and gap filling. Use when processing raw LC-MS data into a feature table for untargeted metabolomics.
- ▌ Skill Creator · biotender-max bundleCreate new skills, modify and improve existing skills, and measure skill performance. Use when users want to create a skill from scratch, edit, or optimize an existing skill, run evals to test a skill, benchmark skill performance with variance analysis, or optimize a skill's description for better triggering accuracy.
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- ▌ Bio Longread Structural Variants · biotender-max bundleDetect structural variants from long-read alignments using Sniffles, cuteSV, and SVIM. Use when detecting deletions, insertions, inversions, translocations, or complex rearrangements from ONT or PacBio data, especially those missed by short-read methods.
- ▌ Self Awareness · biotender-maxClaude Science's own session database schema and SDK surface for introspection via host.query(). Load this when you need to query your own conversation history, token usage, cost accounting, execution log, or artifact metadata beyond what host.frames()/host.artifacts() provide — e.g. "how many tokens has this session used", "what was my last tool call", "list every file I've written", "where are messages stored", "what tables can I query", "inspect frames.context_data", or any time you're about to PRAGMA-probe the Claude Science metadata DB to discover its schema.
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