BioTender-max
- 258 skills
- 0 followers
- 3 days ago last updated
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- ▌ Jungian Psychologist · biotender-max bundleExpert in Jungian analytical psychology, depth psychology, shadow work, archetypal analysis, dream interpretation, active imagination, addiction/recovery through Jungian lens, and the individuation process - grounded in primary sources and clinical frameworks. Activate on 'Jung', 'Jungian', 'shadow work', 'archetypes', 'dream interpretation', 'active imagination', 'individuation', 'anima', 'animus', 'collective unconscious', 'addiction', 'recovery', 'spiritus contra spiritum'. NOT for therapy or diagnosis (only licensed analysts diagnose), active psychosis, severe dissociation, or replacing the relational container of actual Jungian analysis.
- ▌ Statistical Analysis · biotender-max bundleGuided statistical analysis: test choice, assumption checks, effect sizes, power, APA reporting. Pick tests, verify assumptions, or format results for publication. Covers frequentist (t-test, ANOVA, chi-square, regression, correlation, survival, count, reliability) and Bayesian. Use statsmodels or pymc-bayesian-modeling to fit.
- ▌ Bio Hi C Analysis Compartment Analysis · biotender-max bundleDetect A/B compartments from Hi-C data using cooltools and eigenvector decomposition. Identify active (A) and inactive (B) chromatin compartments from contact matrices. Use when identifying A/B compartments from Hi-C data.
- ▌ Bio Ribo Seq Ribosome Periodicity · biotender-max bundleValidate Ribo-seq data quality by checking 3-nucleotide periodicity and calculating P-site offsets. Use when assessing library quality or determining read offsets for downstream analysis.
- ▌ Bio Ecological Genomics Species Delimitation · biotender-max bundleDelimits species boundaries from molecular data using distance-based (ASAP), tree-based (bPTP, GMYC), and coalescent (BPP) methods. Compares multiple delimitation results with delimtools. Use when delineating putative species from DNA barcoding data, resolving cryptic species complexes, or validating taxonomic assignments. Emphasizes multi-method consensus following integrative taxonomy best practice.
- ▌ Bio Epidemiological Genomics Variant Surveillance · biotender-max bundleAssign pathogen lineages and track variants using Nextclade and pangolin for viral surveillance. Monitor variant prevalence and identify emerging variants of concern. Use when classifying viral sequences, tracking lineage dynamics, or monitoring for variants of concern.
- ▌ Figure Composer · biotender-max bundleCompose one publication-grade multi-panel figure. Entry from a one-line claim + data refs, OR from an existing figure via `derive_outline(png)`. Runs a per-figure loop: outline (12-col grid, per-panel ask + label_budget) → fan-out one sub-agent per panel (each loads `figure-style`) → tile + stamp letters → adversarial composite review with two-tier feedback (Tier-1 outline_revisions / Tier-2 per-panel violations) → regen affected panels, ≤3 rounds. Loads panel_task / compose_figure / compose_crops / composite_review_task / derive_outline into the kernel. For one standalone plot use `figure-style`; for whole-paper figure ordering use `paper-narrative`.
- ▌ Paper Narrative · biotender-max bundleJudge and reshape the STORY a paper's figures tell. Input is the work itself — manuscript (or abstract) + figure deck — no hand-written brief. `derive_paper_brief(abstract, captions)` extracts pitch/vision/per-figure-claims; a handling-editor reviewer on the full deck returns hook_verdict (would Fig 1 make me send this for review?), arc (hook→mechanism→evidence→application), figure_moves (panels in the wrong figure), missing_panels (concrete analyses to RUN), kill_list, and boldest_defensible_fig1. Hands per-figure claims to `figure-composer`. Load when writing or revising a paper.
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- ▌ Bio Ecological Genomics Conservation Genetics · biotender-max bundleAssesses genetic health of populations for conservation using effective population size estimation (GONE2 for recent Ne trajectory, NeEstimator for contemporary Ne, Stairway Plot 2 and PSMC for historical Ne), F-statistics (hierfstat), runs of homozygosity (detectRUNS), and genetic diversity metrics. Use when estimating effective population size, detecting inbreeding or bottlenecks, or assessing genetic diversity in threatened species from microsatellite or SNP data.
- ▌ Bio Metagenomics Kraken · biotender-max bundleTaxonomic classification of metagenomic reads using Kraken2. Fast k-mer based classification against RefSeq database. Use when performing initial taxonomic classification of shotgun metagenomic reads before abundance estimation with Bracken.
- ▌ Bio Spatial Transcriptomics Spatial Preprocessing · biotender-max bundleQuality control, filtering, normalization, and feature selection for spatial transcriptomics data. Calculate QC metrics, filter spots/cells, normalize counts, and identify highly variable genes. Use when filtering and normalizing spatial transcriptomics data.
- ▌ Bio Spatial Transcriptomics Spatial Visualization · biotender-max bundleVisualize spatial transcriptomics data using Squidpy and Scanpy. Create tissue plots with gene expression, clusters, and annotations overlaid on histology images. Use when visualizing spatial expression patterns.
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- ▌ Pymc Bayesian Modeling · biotender-max bundleBayesian modeling with PyMC 5: priors, likelihood, NUTS/ADVI sampling, diagnostics (R-hat, ESS), LOO/WAIC comparison, prediction. Hierarchical, logistic, GP variants; predictive checks.
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- ▌ Bio Single Cell Multimodal Integration · biotender-max bundleAnalyze multi-modal single-cell data (CITE-seq, Multiome, spatial). Use when working with data that measures multiple modalities per cell like RNA + protein or RNA + ATAC. Use when analyzing CITE-seq, Multiome, or other multi-modal single-cell data.
- ▌ Compute Env Setup · biotender-max bundleSet up a compute environment on a remote provider so Claude Science jobs can run there. Covers direct SSH/conda hosts, Slurm clusters, container-via-bridge runners, and managed-API providers (Modal, GCP, RunPod). Use when standing up a new provider, porting an env to a different backend, adding a tool that needs its own software stack, or wiring weight caches. Triggers on "new compute provider", "set up env on", "port env to", "build GPU image", "weight cache", "compute_details", "conda env on the box", "apptainer on slurm".
- ▌ Literature Review · biotender-max bundleFind, verify, and synthesize scientific literature — from "what's the seminal paper for X" through full multi-source reviews. Covers grounding claims in real retrieved sources, avoiding fabricated citations, handling retractions, and calibrating confidence to evidence strength.
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- ▌ Bio Read Qc Contamination Screening · biotender-max bundleDetect sample contamination and cross-species reads using FastQ Screen. Screen reads against multiple reference genomes to identify bacterial, viral, adapter, or sample swap contamination. Use when suspecting cross-contamination or working with samples prone to microbial contamination.
- ▌ Indication Dossier · biotender-max bundleGenerate a therapeutic indication dossier. Covers the patient population, epidemiology, disease biology, standard of care, regulatory precedent, and landmark clinical trials.
- ▌ Remote Compute Ssh · biotender-maxSubmit→wait_for_notification→harvest workflow for the user's SSH/SLURM hosts. Load once you've decided to dispatch remote.
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- ▌ Crisis Response Protocol · biotender-maxHandle mental health crisis situations in AI coaching safely. Use when implementing crisis detection, safety protocols, emergency escalation, or suicide prevention features. Activates for crisis keywords, safety planning, hotline integration, and risk assessment.
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- ▌ Binder Design Campaign Manager · biotender-max bundleBinder design campaign planning, monitoring, and troubleshooting. Use this skill when: (1) Planning a complete binder design campaign, (2) Converting high-level goals into runnable pipelines, (3) Assessing campaign health and pass rates, (4) Diagnosing why designs are failing QC, (5) Estimating time, cost, and expected yields, (6) Selecting between design tools for a specific target. This skill orchestrates the other protein design tools. For individual tool parameters, use the specific tool skills.