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Creates a new graphics format spec (custom canvas dimensions + content rules) and publishes it to the Gooseworks library so any agent can render against it. Use when the existing community formats (carousel, story, infographic, slides, poster, chart, tweet, plus community additions) don't fit the user's canvas — e.g., LinkedIn banner 1584×396, story cover 1080×1920, event flyer 8.5×11in. Mirrors goose-graphics-create-style but for formats.

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AI-agent-powered lead enrichment using Sixtyfour as primary source. Takes an email (+ optional name) and returns comprehensive person + company data with funding, AI/B2B classification, and full error visibility. Higher cost (~$0.20/lead) but simpler architecture.

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Analyze a company's published content to extract their brand voice, writing style, and tone guidelines. Reads 10-20 of their best content pieces and produces a brand voice profile covering tone, vocabulary level, sentence structure, formatting patterns, CTAs, and target persona. Useful before writing outreach, content, or campaigns that should match a client's existing voice.

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Final QC gate for a rendered 9:16 video ad, run before it is published. One script checks what a machine can decide — exact 1080x1920 size, a hook that moves and speaks in the first second, no frozen stretches, no dead air, no black frames, the brand's real logo on the end card (never a favicon, never a redrawn or wrong logo), end-card colours near the brand palette — and builds one contact sheet (frames with the TikTok/Reels UI safe zones shaded, beside the logo, product images and a font specimen) for the checks that need eyes — font, product likeness, product consistency across scenes, safe zones. A declared silent-text profile covers silent, text-led formats such as kinetic text (no audio track needed, short blank beats between text beats allowed within fixed bounds). Exit 0 PASS / 2 FAIL / 3 ERROR. Use on every finished video master before pinning it.

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Build the deterministic PIL pill overlays for a 'perfect-score + proof-points' UGC video ad (white 10/10 score header with a medal + orange sub with a finger-down + 3-4 green-check proof pills) and composite them onto a base clip in a diagonal L->R->L->R cascade, then mux the music bed into master-final.mp4. Config-driven (config.json), 1080x1920 9:16, FREE and deterministic (no paid calls, text stays pixel-crisp). Use for the overlay-proof-points format; the base clip + music come from separate paid capabilities.

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Watch a brand's own product footage (screen recording, product film), pick the moment that proves each line with the user, and render those picks as a product layer — free, local. survey.py turns footage into timestamped contact sheets + scene cuts + motion so the agent can actually look at it; the agent writes a cut list (beat → source window + framing); preview.py draws it as a review sheet the user corrects round by round; cut.py renders the approved list into a silent 1080x1920 layer with the creator's area left as a plate. Also frames footage as a filmed screen (keystone, bezel, handheld drift) with dissolves between beats, and takes still screenshots as sources. Use for any format that shows real product footage beside, between or instead of a creator (split-screen, screen inserts, walkthroughs).

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Assemble an absurdist animated-explainer video ad (~38s, 9:16) from per-scene i2v clips + their measured VO windows — retime each clip to its VO, re-encode every segment to identical 30fps/libx264/yuv420p so the concat demuxer never drops frames, concat, build a REAL-product PIL end card (never AI) held static, mix VO (loudnorm I=-14) under music (loudnorm I=-26, volume 0.62, amix normalize=0), and burn libass captions last. FREE deterministic assembly (bash-free, Python + ffmpeg + PIL); the recipe supplies the clips, VO, music, product photo, palette, and caption table and gates the paid keyframe/clip/VO/music calls to their own capabilities. Use for the absurdist-explainer format.

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Assemble a myth-vs-fact kinetic-typography explainer video ad (≈29.5s, 9:16) from N myth/fact pairs + hook / turn / punch copy + palette + a brand end-card PNG + a VO track — a hook, 3 red-strike MYTH cards that flip to teal-check FACT cards (per-line strikethrough that crosses EVERY wrapped line), a "what actually works" turn, an optional proof reveal, a punch line, and a static end card. DETERMINISTIC assembly with ZERO AI-gen visuals — HTML hyperframes rendered frame-exact via Playwright (`window.renderAt(t)`, animation a pure function of beat-local time), Whisper beat-snap to VO word onsets, concat at a uniform fps, karaoke `.ass` captions burned last (suppressed on the proof + end-card beats), and a VO + optional music mix (music −20 dB, `amix normalize=0`, tail fade). FREE (Python + Playwright + ffmpeg); the recipe supplies the copy / palette / end-card / VO and gates the paid VO / music / Whisper calls to their own capabilities. Use for the myth-vs-fact format.

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Assemble a silent, music-led 3-world product-tour ad — trim and hard-cut-concat the per-world WIDE-arrival + top-down-macro clips, composite the HTML/Playwright brand end card (approved headline + handwritten product labels + arrows) over an AI flat-lay background, and mux one music bed into a 720x1280 web master. FREE, deterministic assembly (Playwright + PIL/HTML + FFmpeg); the recipe supplies the config and gates the paid clip/background/music calls. Use for the multiworld-product-tour format.

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Infer or annotate TCR antigen specificity by unsupervised clustering (TCRdist/tcrdist3, GLIPH2, clusTCR, GIANA) and database lookup (VDJdb, IEDB, McPAS-TCR), and rank candidates with supervised predictors (ERGO-II, NetTCR-2.x, pMTnet) under explicit caveats. Encodes the central truth that general TCR-epitope prediction for UNSEEN epitopes essentially does not work (collapses to near-random; IMMREP22, Grazioli 2022) because labeled data is dominated by a few immunodominant epitopes and there is no true negative set — so clustering for discovery is the honest task and de-novo binding needs wet-lab validation. Use when annotating TCR specificity or grouping a repertoire. Epitope/MHC context lives in mhc-binding-prediction.

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Structures biological experiments so inference is valid by construction, covering Fisher's principles (randomization, replication, local control), the experimental-vs-observational unit distinction and pseudoreplication (Hurlbert 1984; Lazic 2018), randomization mechanics (complete, restricted, stratified, rerandomization, run-order), blocking layouts (randomized complete block, Latin square, incomplete block), factorial designs and interactions, and the split-plot/nested error strata hidden inside multi-batch genomics. Use when deciding the experimental unit and what counts as a replicate, planning randomization and run order, choosing a blocked/factorial/split-plot/nested layout, avoiding pseudoreplication in cell-culture or animal studies, or specifying the random-effects structure of the analysis model. For assigning samples to sequencing batches/lanes/plates and batch-effect correction see experimental-design/batch-design; for regulated clinical-trial randomization see clinical-biostatistics.

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Detect distant homologs using profile and structure-aware methods that go beyond standard BLAST. Use when sequence identity falls into the twilight zone (<35% pairwise), when BLAST fails to find homologs that should exist, when working at metagenomic scale (DIAMOND, MMseqs2), or when structure beats sequence (Foldseek). Covers PSI-BLAST (iterative PSSM), jackhmmer (iterative HMM), HHblits/HHsearch (profile-profile), DIAMOND, MMseqs2, and Foldseek (3Di structural alphabet, van Kempen 2024).

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Run remote BLAST searches against NCBI servers using Biopython Bio.Blast.NCBIWWW. Use when identifying unknown sequences, finding homologs, picking the correct BLAST program (blastn/blastp/blastx/tblastn/tblastx/psiblast/megablast/dc-megablast), interpreting Karlin-Altschul E-values, avoiding the max_target_seqs trap (Shah 2019), choosing composition-based statistics, or limiting searches by organism. Covers RID lifecycle, database choice (nt/nr/refseq_select/swissprot), word-size and CBS taxonomy.

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Find cross-database references between NCBI databases using Biopython Bio.Entrez (ELink). Use when navigating gene to protein/structure, sequence to publication, PubMed to GEO, BioProject to SRA runs, or discovering all link relationships for a record. Covers linkname semantics, cmd= variants, asymmetric link warnings, neighbor_history for >200 input IDs, and per-database link tables.

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Download large datasets from NCBI efficiently using EPost, history server, batching, rate limiting, and retry logic. Use when bulk-fetching tens of thousands of sequences, pulling all results of a large ESearch, designing reproducible pipelines, comparing E-utilities to NCBI Datasets v2 CLI, or implementing checksum-validated downloads. Encodes WebEnv TTL (~8h), EPost 200-ID limit, retmax caps, parallelization design, and integrity verification.

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Runs JACKS (Joint Analysis of CRISPR/Cas9 Knockout Screens; Allen et al 2019 Genome Research) which models per-sgRNA log-fold-change as the product of a treatment-dependent gene-essentiality term and a treatment-independent guide-efficacy term. Covers the Bayesian decomposition math, the hierarchical efficacy prior shared across screens performed with the same library, when JACKS outperforms MAGeCK (multi-screen joint analysis, libraries with broad efficacy variance) and when it does not (single screen, novel libraries with no prior efficacy), library-reuse efficacy transfer, downstream essentiality interpretation, and the 2.5x sample-size reduction enabled by efficacy-aware testing. Use when running multiple screens with the same library, when guide-level noise is suspected to dominate per-gene signal, when reusing published essentiality reference screens for efficacy priors, or when comparing screens performed across cell lines that share library but differ biologically.

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Plot per-group distributions of continuous data using boxplots, violins, beeswarms, quasirandom jitter, and raincloud plots with sample-size honesty (Weissgerber 2015), KDE-bandwidth awareness, and N-aware encoding choices. Use when comparing distributions across a small number of groups — expression per cluster, biomarker per arm, scores per condition — and the bar-of-mean default is misleading.

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Designs and analyzes pooled prime-editor (PE) screens for installing precise genetic variants without bystander confounding. Covers pegRNA design with PRIDICT and PRIDICT2 for predicting per-pegRNA editing efficiency, pegRNA architecture (spacer + scaffold + PBS + RTT), PE2/PE3/PE3b/PEmax variants, MOSAIC in situ saturation mutagenesis, the PRIME pooled-screen methodology (Ren 2023; ~3,699 ClinVar variant screens), chromatin context as a major locus-level determinant of PE efficiency, scaffold-incorporation and indel byproduct quantification with CRISPResso2, and the cross-modal validation strategy of PE + base-editor screens for variant function. Use when designing a pegRNA library for variant installation, choosing between BE and PE for a specific edit, predicting pegRNA efficiency before library synthesis, analyzing PE screen output, distinguishing intended-edit from scaffold-incorporation, or scaling PE screens to thousands of variants.

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Extracts, filters, annotates, and exports differential expression results from DESeq2 or edgeR with proper handling of padj=NA (independent filtering, Cook's outliers, all-zero), multiple-testing correction choice (BH vs Storey q-value vs IHW vs lfsr), TREAT vs post-hoc fold-change filtering, p-value histogram diagnostics, gene annotation via org.db/biomaRt/mygene, GSEA preranked input, ORA background construction, replication reality (Schurch 2016 small-n result), and SABV/sex-stratified reporting. Use when extracting and interpreting DE results, troubleshooting padj=NA, choosing FDR method, preparing ranked lists for pathway analysis, annotating gene IDs, or comparing DESeq2 vs edgeR outputs.

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Analyzes pooled CRISPR screens with MAGeCK (Li et al 2014), covering count generation (mageck count), the RRA two-condition workflow (mageck test using alpha-RRA over per-sgRNA negative-binomial p-values), the MLE multi-condition workflow (mageck mle with explicit design matrix and beta-score output), normalization choice (median vs total vs control-sgRNA vs spike-in), sgRNA efficiency injection, paired-sample testing, time-course design, drug-screen versus dropout-screen design matrices, MAGeCKFlute and MAGeCK-VISPR downstream visualization, and decision logic for when to use MAGeCK vs JACKS / BAGEL2 / drugZ / Chronos. Use when running a fresh CRISPR screen analysis, picking RRA vs MLE for the experimental design, choosing a normalization method from QC signatures, debugging MLE convergence failure or NaN beta scores, comparing MAGeCK output across tools, or building a batch-aware multi-cell-line / multi-condition MLE design matrix.

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Detect positive (diversifying / episodic / pervasive) selection using codon dN/dS frameworks. Implements PAML codeml site models (M0/M1a/M2a/M7/M8/M8a), branch models, branch-site model A (Zhang 2005), and HyPhy methods (BUSTED, BUSTED-S, BUSTED-MH, BUSTED-PH, MEME, FEL, FUBAR, aBSREL, SLAC, RELAX, GARD, FUBAR-MH). Includes McDonald-Kreitman framework (asymptotic alpha, impMKT, polyDFE, DFE-alpha, GRAPES) for within-species + divergence inference, RERconverge for trait-correlated rate shifts, CSUBST for convergent substitution, and PhyloAcc for accelerated noncoding evolution. Use when testing adaptive evolution at codons, branches, or full gene; running GARD recombination pre-screen; controlling alignment-error and gBGC false positives; reconciling PAML vs HyPhy results; or performing genome-scale selection scans.

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Analyzes CRISPR drug-modifier (chemogenomic) screens with drugZ (Colic et al. 2019 Genome Med), a bidirectional Z-score method that identifies synthetic-lethal sensitizing genes and resistance-conferring suppressor genes from vehicle vs drug comparisons. Covers vehicle-anchored design (not Day-0), the bidirectional Z math giving greater sensitivity to small-effect hits than MAGeCK / STARS / edgeR / RIGER on drug screens, per-gene sumZ and normZ, synth (sensitizer) vs supp (suppressor) FDR, multi-dose handling, integration with control sgRNAs, and comparison with MAGeCK MLE with dose covariate. Use when running a drug-modifier CRISPR screen, identifying sensitizing or resistance genes for a drug candidate, choosing drugZ vs MAGeCK MLE for chemogenomic analysis, troubleshooting low-effect drug screens where MAGeCK lacks sensitivity, or designing a drug-screen layout (vehicle vs drug arms).

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Build and analyze pangenomes for prokaryotes (Panaroo, PPanGGOLiN, PEPPAN, GET_HOMOLOGUES, anvi'o pangenomics) and eukaryotes (Minigraph-Cactus, PGGB, vg pangenome graphs). Implement Tettelin core/accessory/cloud genome decomposition (Tettelin 2005), Heap's law open/closed pangenome modeling, gene presence/absence GWAS (Scoary, pyseer), pangenome graph variant calling (vg, PanGenie), and structural-variation graph indexing. Use when assembling species- or genus-level pan-gene catalogs, separating core from accessory/shell/cloud genes, testing gene-content associations with phenotypes, building pangenome graphs from haplotype-resolved assemblies, calling SVs from pangenome graphs, or selecting between bacterial-pangenome and eukaryotic-pangenome workflows.

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Quantifies CRISPR editing outcomes with CRISPResso2 (Clement 2019 Nat Biotechnol) across Cas9-nuclease (indels, HDR), CBE and ABE base editors (target conversion + bystander), and prime editor (pegRNA-templated) modes. Covers single-amplicon (CRISPResso), multi-sample batch (CRISPRessoBatch), pooled-amplicon (CRISPRessoPooled), WGS off-target (CRISPRessoWGS), and sample-comparison (CRISPRessoCompare) workflows; quantification-window math that controls what is called edited; substitution-vs-indel diagnostic to distinguish BE from Cas9 contamination; MMEJ deletion pattern interpretation; allele-frequency tables; and failure modes from amplicon misalignment or contamination. Use when quantifying editing from amplicon sequencing, choosing CRISPResso mode by design, distinguishing intended edits from bystanders and indel byproducts, debugging low-alignment runs, or generating publication-grade editing reports.

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