Browse Skills — Page 131

genetic_counseling_report

InternScience/scp

Genetic Counseling Variant Report - Generate variant report for genetic counseling: VEP, ClinVar, gene phenotype, and literature evidence. Use this skill for clinical genetics tasks involving get vep hgvs clinvar search get phenotype gene pubmed search. Combines 4 tools from 2 SCP server(s).

geniml

K-Dense-AI/scientific-agent-skills

This skill should be used when working with genomic interval data (BED files) for machine learning tasks. Use for training region embeddings (Region2Vec, BEDspace), single-cell ATAC-seq analysis (scEmbed), building consensus peaks (universes), or any ML-based analysis of genomic regions. Applies to BED file collections, scATAC-seq data, chromatin accessibility datasets, and region-based genomic feature learning.

genmedia

fal-ai-community/genmedia-cli

>

genome_annotation

InternScience/scp

Genome Annotation Pipeline - Annotate a genome: NCBI annotation report, Ensembl gene lookup, UCSC tracks, and KEGG pathway links. Use this skill for genomics tasks involving get genome annotation report get lookup symbol list tracks kegg link. Combines 4 tools from 4 SCP server(s).

genome-annotation-annotation-qc

swaruplab/operon

Assesses the quality and completeness of a genome annotation with BUSCO (conserved single-copy ortholog recovery), OMArk (proteome completeness, consistency, and contamination), CheckM2 (prokaryotic completeness/contamination), and a gene-set sanity panel (gene count, mono-exonic fraction, protein-length distribution, mRNA:gene ratio, coding density). Covers the assembly-BUSCO-vs-proteome-BUSCO diagnostic, what BUSCO-Duplicated really means, why gene count is a vanity metric, and the QC of transferred annotations. Use when judging whether an annotation is good enough to publish or submit, diagnosing a suspect annotation, or comparing annotation completeness across pipelines.

genome-annotation-annotation-transfer

swaruplab/operon

Transfers gene annotations between genome assemblies via coordinate liftover (UCSC liftOver, CrossMap for same-species version updates) or feature/sequence projection (Liftoff for same/close species, miniprot for protein-level cross-species, TOGA/GeMoMa/CAT for distant clades). Covers the coordinate-vs-projection decision by divergence, why a successful lift is not biological confirmation, reference bias, the silent-dropping of unmapped features, build/PAR/MHC/inversion hazards, and transfer-vs-de-novo validation. Use when annotating a new assembly of a species with an existing reference, harmonizing coordinates across builds, or mapping annotations across related species.

genome-annotation-eukaryotic-gene-prediction

swaruplab/operon

Predicts protein-coding gene structures (exons, introns, UTRs) in eukaryotic genomes with BRAKER3 (RNA-seq + protein evidence), BRAKER1/BRAKER2, GALBA (protein-only), Funannotate (fungi), GeMoMa (homology projection), or Helixer/Tiberius (deep-learning ab initio). Covers the evidence-first tool decision, mandatory soft-masking, the training-set-quality-dominates principle, OrthoDB clade-partition selection, the one-isoform-per-locus and missing-UTR traps, merge/split errors, and reference bias against orphan genes. Use when annotating a newly assembled eukaryotic genome, choosing a gene-prediction pipeline based on available evidence, or diagnosing a poor annotation.

genome-annotation-functional-annotation

swaruplab/operon

Assigns GO terms, Pfam/InterPro domains, KEGG orthologs, EC numbers, and product names to predicted proteins using eggNOG-mapper (orthology), InterProScan (domain signatures), and KofamScan (KEGG), routing specialized functions to dbCAN/antiSMASH/AMRFinderPlus/SignalP. Covers the orthology-vs-domain-vs-homology paradigms, the annotation-error percolation cascade, domain-presence-is-not-function, GO IEA circularity in enrichment, evidence tiering, and bit-score/coverage thresholds. Use when adding functional annotation to predicted genes, choosing between eggNOG-mapper and InterProScan, or judging how much to trust a functional label.

genome-annotation-ncrna-annotation

swaruplab/operon

Identifies non-coding RNAs (tRNA, rRNA, snoRNA, snRNA, riboswitches, sRNAs) using Infernal covariance-model search against Rfam, tRNAscan-SE 2.0 for tRNA, barrnap for rRNA, and ARAGORN for tmRNA, plus the small-RNA-seq boundary for miRNA and the transcript-assembly boundary for lncRNA. Covers the structure-conserved-not-sequence-conserved principle (why BLAST fails), GA-threshold and clan-competition correctness, tRNAscan-SE domain modes and pseudogene flags, rDNA copy-number collapse, and why homology annotation is a recall floor. Use when performing genome-wide ncRNA annotation, choosing the right tool for an RNA class, or interpreting ncRNA counts.

genome-annotation-prokaryotic-annotation

swaruplab/operon

Annotates bacterial and archaeal genomes (isolates, MAGs, plasmids) with Bakta (active versioned databases, NCBI-compliant output) or Prokka (legacy), producing GFF3/GenBank/EMBL/FASTA with INSDC locus tags. Covers Bakta-vs-Prokka-vs-PGAP-vs-DFAST choice, light-vs-full database tiers, translation-table selection (11/4/25), archaeal and leaderless-gene caveats, the small-ORF blind spot, pseudogene-vs-phase-variation, the pangenome re-annotation trap, and submission compliance. Use when annotating a newly assembled prokaryotic genome, choosing an annotation tool, re-annotating a collection for pangenomics, or preparing annotations for NCBI/DDBJ submission.

genome-annotation-repeat-annotation

swaruplab/operon

Discovers, classifies, and masks repetitive elements and transposable elements with RepeatModeler2 (de novo family library), RepeatMasker (masking against a library), EDTA (plant/structural TEs), or EarlGrey (auto-curating wrapper), and quantifies TE expression from RNA-seq with TEtranscripts/SQuIRE. Covers de-novo-library-as-curation-project, soft-vs-hard masking, the domesticated-gene over-masking massacre, Dfam-vs-RepBase, TE classification (Class I/II, family-vs-copy), Kimura repeat landscapes, LAI, and the RNA-seq multimapping problem. Use when masking repeats before gene prediction, building a TE library for a non-model genome, or analyzing transposable-element content or expression.

genome-assembly-assembly-polishing

swaruplab/operon

Decides whether and how to polish a draft genome assembly to raise consensus accuracy (QV) with read-type-matched tools - Racon and medaka (ONT consensus), dorado polish, Polypolish and pypolca (Illumina, repeat-aware), Pilon (legacy short-read), NextPolish/NextPolish2, Hapo-G (haplotype-aware), ntEdit, and DeepPolisher/PEPPER-Margin-DeepVariant for human. Covers the do-not-polish-HiFi rule, the medaka basecaller-model footgun, held-out Merqury QV as the only honest stop signal, and the haplotype-collapse trap. Use when correcting homopolymer indels or residual SNPs in a long-read assembly, deciding if a HiFi assembly needs polishing, or choosing an ONT vs hybrid vs short-read polishing chain.

genome-assembly-assembly-qc

swaruplab/operon

Evaluates genome assembly quality across the three orthogonal axes - contiguity (QUAST auN/NG50/NGx, not bare N50), completeness (BUSCO/compleasm gene-space plus Merqury k-mer completeness), and correctness (reference-free Merqury QV, Inspector/CRAQ structural errors, asmgene false-duplication/collapse). Covers why N50 is the most-gamed metric, why QV measured on the polishing reads is circular, distinguishing uncollapsed haplotigs from real WGD, and the EBP/VGP 6.C.Q40 standard. Use when judging whether an assembly is good enough to annotate or publish, comparing assemblers, diagnosing a fragmented or duplicated assembly, or assessing a phased diploid assembly.

genome-assembly-contamination-detection

swaruplab/operon

Detects and removes contamination in genome assemblies via two disjoint workflows - foreign-sequence screening of a single-organism (eukaryote/isolate) assembly with NCBI FCS-GX (GenBank-submission-mandatory), FCS-adaptor, and BlobToolKit blob plots; and MAG/bin quality assessment with CheckM2 plus GUNC (chimerism) plus GTDB-Tk taxonomy, judged against MIMAG. Covers why CheckM2 alone is blind to disjoint-marker chimeras, the FCS-GX RAM wall, organelle/NUMT triage, strain heterogeneity, and the HGT-vs-contamination (tardigrade) trap. Use when screening an assembly for foreign contamination before GenBank submission, assessing MAG completeness/contamination/chimerism, deciding which contigs to remove, or distinguishing real HGT from contaminant contigs.

genome-assembly-genome-profiling

swaruplab/operon

Profiles a genome from raw reads BEFORE assembly with a k-mer spectrum (KMC or Jellyfish histogram), then models it with GenomeScope2 to estimate genome size, heterozygosity, repeat content, and ploidy, and Smudgeplot to infer ploidy from heterozygous k-mer pairs (diploid AB vs triploid AAB vs tetraploid AABB). Covers choosing k via Merqury best_k.sh, the k-mer-coverage vs sequencing-coverage confusion, reading het/repeat/contamination/organelle peaks, why noisy ONT must not be used for counting, and how the estimate becomes the NG50 denominator, the Flye -g value, the hifiasm --hom-cov/purge setting, and the 1.5-2x-too-big haplotig sanity check. Use when starting any de novo assembly, deciding whether short reads can work, estimating genome size for an unknown organism, diagnosing ploidy, or sanity-checking an assembly's size against expectation.

genome-assembly-hifi-assembly

swaruplab/operon

Assembles haplotype-resolved diploid and telomere-to-telomere (T2T) genomes from PacBio HiFi reads with hifiasm (HiFi-only, Hi-C, or trio phasing) and verkko (HiFi + ultralong ONT for T2T), extracting contigs from GFA and routing phasing QC to k-mer/trio metrics. Covers why a primary assembly is a haplotype mosaic that exists in no cell, partial-vs-full phasing (the .bp. vs .dip. filename convention), the purge-default trap on inbred samples, the --hom-cov coverage-estimate alarm, and verkko-vs-hifiasm for T2T. Use when assembling a diploid eukaryote from HiFi, phasing haplotypes with parents (trio) or Hi-C, deciding whether to chase T2T, or diagnosing switch errors invisible to N50/BUSCO/QV.

genome-assembly-long-read-assembly

swaruplab/operon

Assembles genomes de novo from noisy long reads (Oxford Nanopore R9/R10/Dorado, PacBio CLR) with Flye (repeat graph), Canu (correct-trim-assemble OLC), NextDenovo, Shasta, Raven, wtdbg2, or miniasm, and reconciles bacterial assemblies into a consensus with Trycycler/Autocycler. Covers matching the input flag to the basecaller era (--nano-hq vs --nano-raw), why a raw long-read assembly is contiguous but low-QV and not finished until polished, haplotig false-duplication and purge_dups, coverage and read-N50 as non-substitutable inputs, and mid-read adapter de-chimerization. Use when assembling a bacterial or eukaryotic genome from ONT or PacBio noisy reads, choosing a long-read assembler, or diagnosing an over-collapsed or duplicated assembly. For PacBio HiFi use hifi-assembly instead.

genome-assembly-metagenome-assembly

swaruplab/operon

Assembles microbial-community sequencing into metagenome-assembled genomes (MAGs) with metaFlye (ONT), metaSPAdes/MEGAHIT (Illumina), and hifiasm-meta/metaMDBG (PacBio HiFi), then recovers genomes via multi-binner consolidation (MetaBAT2, MaxBin2, CONCOCT, SemiBin2, VAMB -> DAS_Tool) and QCs them against MIMAG with CheckM2, GUNC, and GTDB-Tk. Covers why a metagenome is not a genome (uneven coverage, micro-diversity, strain collapse to consensus), differential-coverage binning, co-assembly vs per-sample, the rRNA-operon collapse that fails short-read MAGs, and strain resolution with inStrain. Use when reconstructing genomes from a microbiome, soil, ocean, or gut community, recovering MAGs, or resolving strain-level variation.

genome-assembly-scaffolding

swaruplab/operon

Orders and orients assembled contigs into chromosome-scale scaffolds from long-range linking data, inserting N-gap spacers (adds no sequence). Covers Hi-C/Omni-C scaffolding (YaHS, SALSA2, 3D-DNA/Juicer), Hi-C read-mapping prerequisites (map each end separately, no mate rescue, dedup, enzyme-aware), reading the contact map for misjoins/inversions/false-duplications, manual curation in Juicebox/PretextView (the VGP/DToL standard), reference-guided scaffolding (RagTag) and its karyotype-erasure hazard, genetic-map (ALLMAPS) and Bionano optical-map integration, chimera-breaking before scaffolding, gap-filling, and telomere/contig-vs-scaffold-N50 QC (tidk). Use when turning contigs into chromosomes with Hi-C, integrating a linkage map or optical map, choosing a scaffolder by available linking data, or judging whether a chromosome-scale assembly is trustworthy.

genome-assembly-short-read-assembly

swaruplab/operon

Assembles a genome de novo from Illumina short reads with SPAdes (isolate/careful/sc/meta/plasmid/rna modes), MEGAHIT (low-memory, huge datasets), Unicycler (bacterial finishing/hybrid), MaSuRCA (large hybrid), ABySS (Bloom-filter), and Platanus (heterozygous diploids), using multi-k de Bruijn graphs. Covers the repeat-resolution limit, why N50 plateaus at the genome not the depth, GenomeScope2 k-mer profiling first, the heterozygosity/haplotig trap, error-correction erasing rare alleles, GC dropout, and NG50/auN/BUSCO reporting. Use when assembling a bacterial isolate, fungal, small-eukaryotic, single-cell, or metagenome genome from Illumina reads, or when deciding whether short reads can even produce the assembly being asked for.

genome-compare

swaruplab/operon

Compare your genome to George Church (PGP-1) and estimate ancestry composition via IBS and EM admixture

genome-engineering-base-editing-design

swaruplab/operon

Designs cytosine (CBE, C-to-T) and adenine (ABE, A-to-G) base-editor guides by positioning the target base at the activity-peak of the editing window (protospacer positions ~5-7, PAM-distal numbering), minimizing bystander edits for product purity, reading dinucleotide context (APOBEC1 TC favored / GC disfavored), and selecting the editor variant (BE4max, ABEmax, ABE8e, YE1/SECURE, TadCBE, CGBE, SpG/SpRY-BE). Covers knockout by premature stop (CRISPR-STOP/iSTOP) and splice-site disruption, the three off-target classes (Cas-dependent, Cas-independent DNA, RNA), outcome prediction (BE-Hive/DeepBE), and the base-vs-prime-vs-HDR decision. Use when installing a transition mutation without a double-strand break, knocking out a gene without indels, or choosing CBE vs ABE. Generic guide scoring, prime editing, and HDR donors are separate skills.

genome-engineering-grna-design

swaruplab/operon

Designs and ranks guide RNAs (sgRNAs) for CRISPR-Cas9/Cas12a gene knockout by scanning a target for PAM sites (NGG SpCas9, NNGRRT SaCas9, TTTV Cas12a, NG SpCas9-NG, near-PAMless SpRY), enumerating candidate spacers, applying hard filters (Pol-III TTTT terminator, 5' G, GC), ranking on-target activity with the context-appropriate model (Rule Set 2/Azimuth for U6/lentiviral, CRISPRscan for T7/embryo, DeepHF for high-fidelity variants, DeepCpf1 for Cas12a), and predicting the indel/frameshift outcome (Bae out-of-frame score, inDelphi, FORECasT, Lindel). Use when selecting sgRNAs to knock out a gene, choosing a nuclease/PAM for a constrained locus, picking which exon to target, or shortlisting guides before an off-target check. Off-target specificity, base/prime editing, and HDR donors are separate skills.

genome-engineering-hdr-template-design

swaruplab/operon

Designs donor/repair templates for precise CRISPR knock-ins -- choosing the format (ssODN, long-ssDNA/Easi-CRISPR, dsDNA/plasmid, AAV6), sizing homology arms, placing the cut within ~10 bp of the edit, and adding a mandatory codon-checked blocking (PAM/seed) mutation so the edited allele is not re-cut. Frames the HDR-vs-NHEJ-vs-MMEJ pathway competition, the MMEJ (PITCh) and homology-independent (HITI/HMEJ) alternatives for post-mitotic cells, ssODN strand/asymmetry choice, phosphorothioate end-protection, and ranked HDR enhancers. Use when designing a donor for a point mutation, epitope/fluorophore tag, allele replacement, or knock-in, or when HDR efficiency is low. Guide design and base/prime editing are separate skills.

genome-engineering-off-target-prediction

swaruplab/operon

Nominates and assesses CRISPR off-target sites genome-wide. Enumerates candidate sites by mismatch and bulge tolerance with Cas-OFFinder/CRISPRitz, ranks them with the published CFD score (SpCas9-only, relative ranker) or MIT/CRISTA/energy models, runs variant-aware screening against gnomAD/individual genomes (CRISPRme), and frames the empirical genome-wide discovery assays (GUIDE-seq, CIRCLE-seq, CHANGE-seq, DISCOVER-seq, Digenome-seq) and high-fidelity nuclease choice (HiFi Cas9, Sniper-Cas9, eSpCas9, SpCas9-HF1). Use when assessing guide RNA specificity, choosing among candidate guides, screening a therapeutic guide against population variation, or planning empirical off-target validation. Distinguishes predicted vs detected vs validated. On-target activity scoring and deaminase (Cas-independent) base/prime-editor off-targets are separate skills.

genome-engineering-prime-editing-design

swaruplab/operon

Designs pegRNAs and nicking guides for prime editing (PE) -- choosing the nick/strand, tuning the primer-binding site (PBS) and reverse-transcription template (RTT) as a per-locus panel, selecting the PE system (PE2/PE3/PE3b/PE4/PE5/PEmax/PE7), adding MMR-evading and PAM-disrupting silent edits, appending epegRNA 3' motifs (tevopreQ1/mpknot), and ranking with PRIDICT/DeepPrime. Covers twinPE/PASTE for large insertions and the prime-vs-base-editing decision. Use when designing a scarless point mutation, small insertion/deletion, or any of the 12 base conversions without a double-strand break, when efficiency is low and MMR inhibition or pegRNA stabilization is needed, or when routing a large insertion to an integrase method. Generic guide scoring and base editing are separate skills.

genome-intervals-bed-file-basics

swaruplab/operon

Handles BED-format genomic intervals (BED3 through BED12, narrowPeak/broadPeak) and the coordinate-system substrate the whole interval category rests on, with bedtools (CLI) and pybedtools/pyranges/pandas (Python). Covers the 0-based half-open vs 1-based-closed convention boundary and the start-1/end-unchanged conversion, the silent failures (chrom-name mismatch, CRLF, lexicographic-vs-version sort under -sorted), genome/chrom.sizes generation, sorting contracts, BED12 block invariants, validation, makewindows, cross-assembly liftover (liftOver/CrossMap), and BED<->VCF/BAM/FASTA conversion. Use when reading, creating, validating, sorting, lifting between genome builds, or converting interval files, preparing inputs for bedtools/tabix/bigBed, or debugging an off-by-one or empty-overlap result.

genome-intervals-bedgraph-handling

swaruplab/operon

Generates, normalizes, and converts bedGraph signal tracks (4-column chrom/start/end/value, 0-based half-open) with bedtools genomecov, deepTools bamCoverage/bamCompare/bigwigCompare, bedtools unionbedg, and UCSC bedGraphToBigWig. Covers why a raw coverage bedGraph is not comparable across samples until normalized, the CPM/RPKM/BPM/RPGC normalization menu and the conserved-total assumption that makes them wrong under a global perturbation, the strict sorted-non-overlapping-chrom.sizes bedGraphToBigWig contract that silently corrupts a bigWig, effective-genome-size selection, and bin-size aliasing. Use when building or normalizing a coverage/signal track from a BAM, comparing tracks across samples or conditions, converting bedGraph to a browser-ready bigWig, or diagnosing a track that looks plausible but reports wrong heights.

genome-intervals-bigwig-tracks

swaruplab/operon

Reads, queries, and writes bigWig indexed binary signal tracks (coverage, fold-change, conservation, methylation-rate) with pyBigWig (Python) and the UCSC Kent tools (bedGraphToBigWig, bigWigToBedGraph, bigWigInfo, bigWigSummary, bigWigAverageOverBed) and deepTools (multiBigwigSummary, computeMatrix, bigwigCompare). Covers the central trap that a wide query returns a precomputed zoom-level summary (by default the mean, which annihilates narrow peaks) not per-base data, when exact=True/values() is mandatory, the NaN-not-zero gap-handling fork, choosing mean vs max vs sum vs coverage by biological question, and the sorted-bedGraph plus chrom.sizes build requirement. Use when extracting signal at regions, computing mean signal per gene/peak, building a browser track from bedGraph, comparing tracks, or building TSS/gene-body metaprofiles.

genome-intervals-coverage-analysis

swaruplab/operon

Computes and interprets sequencing read depth and coverage over a genome, windows, or target regions with mosdepth (windowed depth, cumulative distribution, --quantize callable BEDs), bedtools genomecov/coverage (bedGraph tracks, per-target stats), samtools depth/coverage (per-base depth, per-contig depth+breadth). Covers the breadth-vs-mean distinction, the cumulative-coverage curve, evenness (CV/Fano/fold-80/Gini), what each tool silently counts (duplicates, secondary/supplementary, MAPQ, read span vs fragment, mate-overlap), the samtools-depth 8000-cap version trap, and the bedtools coverage -a/-b orientation flip. Use when assessing sequencing adequacy, building coverage tracks, computing breadth at a depth threshold, defining callable regions, or QCing target-capture uniformity.

genome-intervals-gtf-gff-handling

swaruplab/operon

Parses, queries, converts, and extracts from GTF and GFF3 gene-model annotation files - walking the gene/transcript/exon/CDS hierarchy with gffutils (queryable SQLite DB), converting formats and extracting transcript/CDS/protein FASTA with gffread, slurping to dataframes with gtfparse/pyranges, and sanitizing malformed files with AGAT. Covers the 1-based-inclusive vs 0-based BED coordinate conversion (start-1 only), deriving implicit features (introns/UTRs/TSS), phase-not-frame, the stop-codon-in-or-out-of-CDS convention, and the chr1-vs-1 seqid and gene-ID-version mismatches that silently produce all-zero count matrices and dropped joins. Use when extracting features or sequences from an annotation, converting GTF<->GFF3 or GTF->BED, traversing the gene tree, or diagnosing a coordinate/provenance mismatch upstream of counting or DE.

genome-intervals-interval-arithmetic

swaruplab/operon

Performs set operations on genomic intervals - intersect (-wa/-wb/-wo/-wao/-loj/-c/-v/-u), subtract (-A), merge (-d, -c/-o), complement, cluster, multiinter, unionbedg, map, and groupby - with bedtools (CLI) and pybedtools/pyranges/bioframe (Python). Covers the sorted-input contract and the -sorted chromosome-order footgun, reciprocal/fractional overlap (-f/-F/-r/-e) and the A-vs-B asymmetry, -split for spliced/BED12/BAM features, and jaccard/fisher as mechanics only. Use when finding overlapping or unique regions between BED/peak/feature files, building consensus peaksets, removing blacklisted regions, transferring annotation values onto intervals, or computing interval-set similarity; route overlap-significance testing to overlap-significance.

genome-intervals-overlap-significance

swaruplab/operon

Tests whether two genomic interval sets overlap (colocalize) more than expected by chance using a permutation test against a structured-genome null model. Covers bedtools fisher (analytic 2x2 screen), bedtools shuffle + jaccard permutation, GAT (isochore/GC-conditioned simulation with FDR), regioneR (flexible permutation, randomizeRegions vs circularRandomizeRegions, localZScore), LOLA (universe-relative Fisher against a region database), and GREAT/rGREAT (regulatory-domain binomial + hypergeometric for ontology-from-regions). Stresses the universe/background choice, matched background, blacklist exclusion, and multiple-testing control. Use when asking whether peaks/regions are enriched at enhancers/TFBS/features, scoring region-set colocalization or region-set enrichment, comparing CNV/SV concordance, or turning an overlap count into a defensible p-value.

genome-intervals-proximity-operations

swaruplab/operon

Performs proximity operations on genomic intervals with bedtools (closest, window, flank, slop) and pybedtools - nearest-feature queries with signed/strand-aware distance, fixed-radius window searches, strand-aware promoter construction, and interval extension. Covers the closest -d/-D a/b/ref/-t/-k/-io/-iu/-id flags, the -D ref strand sign-flip, silent chromosome-end clipping in slop/flank, -t all tie double-counting, and the critical distinction between a geometry answer (nearest TSS) and a biology answer (which gene an element regulates). Use when assigning peaks or variants to genes, defining promoters from a gene model, building distance-to-TSS distributions, finding features within a window, or extending intervals - and when deciding whether nearest-gene is a fair prior (GWAS locus) or a trap (distal enhancer).

genotoxic

trailofbits/skills

Graph-informed mutation testing triage. Parses codebases with Trailmark, runs mutation testing and necessist, then uses survived mutants, unnecessary test statements, and call graph data to identify false positives, missing test coverage, and fuzzing targets. Use when triaging survived mutants, analyzing mutation testing results, identifying test gaps, finding fuzzing targets from weak tests, running mutation frameworks (including circomvent and cairo-mutants), or using necessist.

genpage

microsoft/power-platform-skills

Creates, updates, and deploys Power Apps generative pages for model-driven apps using React v17, TypeScript, and Fluent UI V9. Orchestrates specialist agents for planning, entity creation, and code generation. Use it when user asks to build, retrieve, or update a page in an existing Microsoft Power Apps model-driven app. Use it when user mentions "generative page", "page in a model-driven", or "genux".

genre-action-combat

arjun988/blender-skills

Art direction for action, hack-and-slash, beat 'em up, and fighting-game readable combat spaces and prop language in Blender.

genre-card-party-idle

arjun988/blender-skills

Art direction for card games, deck builders, party games, idle/incremental, educational, and rhythm game presentational spaces in Blender.

genre-creator

bitwize-music-studio/claude-ai-music-skills

Create new genre documentation files for the bitwize-music genre library. Use when the user wants to add a genre, says "/genre-creator", "neues Genre erstellen", "Genre hinzufuegen", "add genre", or asks to create genre documentation. Takes a genre name as argument.

genre-metroidvania-roguelike

arjun988/blender-skills

Art direction for metroidvania, roguelike, and roguelite games in Blender with biome gates, room modules, and run-readable props.

genre-narrative-vn

arjun988/blender-skills

Art direction for visual novel, interactive movie, walking simulator, and story-driven presentation spaces in Blender.

genre-open-world-sandbox

arjun988/blender-skills

Art direction for open world and sandbox games in Blender with biome landmarks, traversable scale, and discovery props.

genre-puzzle-platformer

arjun988/blender-skills

Art direction for puzzle and platformer games in Blender with readable interactables, jump volumes, and clear hazard language.

genre-racing-sports

arjun988/blender-skills

Art direction for racing and sports games in Blender with track landmarks, stadium kits, and high-speed readability.

genre-rpg

arjun988/blender-skills

Art direction for RPG, JRPG, CRPG, ARPG, and MMORPG worlds in Blender including loot rarity reads and region identity.

genre-shooter

arjun988/blender-skills

Art direction for FPS, TPS, shooter, battle royale, and extraction-shooter maps and props in Blender with sightline and cover language.

genre-soulslike

arjun988/blender-skills

Art direction for soulslike games in Blender with monumental melancholy spaces, fog gates, bonfire landmarks, and lethal readability.

genre-stealth

arjun988/blender-skills

Art direction for stealth-game spaces in Blender with shadow volumes, patrol-friendly layouts, and concealment materials.

genre-strategy-sim

arjun988/blender-skills

Art direction for strategy, RTS, turn-based strategy, tower defense, MOBA, city builder, colony sim, and simulation games in Blender.

genre-survival

arjun988/blender-skills

Art direction for survival and survival-horror gameplay spaces in Blender emphasizing resource props, crafting readability, and tension routes.

geo-agent

aAAaqwq/AGI-Super-Team

Automated GEO (Generative Engine Optimization) agent for boosting brand visibility in AI search engines. Manages keywords, researches real competitors, generates comparison articles with target brand prominence, auto-publishes to Chinese content platforms (Zhihu/Baijiahao/Sohu/Toutiao), monitors AI search engine indexing, and reports results. Use when: user wants GEO automation, AI search optimization, multi-platform article publishing, or brand visibility in AI answers.

geo-content-optimizer

aaron-he-zhu/aaron-marketing-skills

Use when the user asks to "optimize for AI citations"; improves citation readiness for ChatGPT, Perplexity, AI Overviews, Gemini, and Claude. Not for structural on-page SEO — use on-page-seo-checker; not for net-new drafting — use content-writer. AI引用优化/GEO优化/AI搜索

geo-database

jaechang-hits/SciAgent-Skills

NCBI 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.

geo-fundamentals

benjaminasterA/antigravity-awesome-skills

Generative Engine Optimization for AI search engines (ChatGPT, Claude, Perplexity).

geo-fundamentals-v2

diegosouzapw/awesome-omni-skills

GEO Fundamentals workflow skill. Use this skill when the user needs Generative Engine Optimization for AI search engines (ChatGPT, Claude, Perplexity) and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

geo-gap-fixer

Varnan-Tech/opendirectory

Audit how often LLMs recommend your brand vs competitors and generate a GEO action plan.

geo-monitor

indranilbanerjee/digital-marketing-pro

Monitor brand AI visibility. Use when: tracking mentions in ChatGPT, Perplexity, Gemini, or AI Overviews.

geo-optimizer

nowork-studio/NotFair

>

geo-search-api

aipoch/medical-research-skills

Search for gene expression DataSets and Profiles in the NCBI GEO database. Use this skill when the user wants to find microarray, RNA-seq, or other genomic data by keywords, organism, author, or specific fields.

geo-toolkit

dkyazzentwatwa/chatgpt-skills

Parse, convert, geocode, visualize, and measure geographic data. Use for address cleanup, geo file conversion, mapping, and distance workflows.

geo-writing

vellum-ai/vellum-assistant

Generates GEO/AEO-optimized articles designed to get AI engines (ChatGPT, Perplexity, Claude, Gemini) to cite your brand. Handles research, writing, and file output. Suggests listicle or head-to-head as starting formats if the user is unsure.

geoapify-automation

ComposioHQ/awesome-claude-skills

"Automate Geoapify tasks via Rube MCP (Composio). Always search tools first for current schemas."

geocodio-automation

ComposioHQ/awesome-claude-skills

"Automate Geocodio tasks via Rube MCP (Composio). Always search tools first for current schemas."

geofeed-tuner

github/awesome-copilot

>

geoffrey-hinton

diegosouzapw/awesome-omni-skills

SKILL: Geoffrey Hinton \u2014 Agente Persona v2.0 workflow skill. Use this skill when the user needs Agente que simula Geoffrey Hinton \u2014 Godfather of Deep Learning, Pr\u00eamio Turing 2018, criador do backpropagation e das Deep Belief Networks and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

geoffrey-hinton-v2

diegosouzapw/awesome-omni-skills

SKILL: Geoffrey Hinton \u2014 Agente Persona v2.0 workflow skill. Use this skill when the user needs Agente que simula Geoffrey Hinton \u2014 Godfather of Deep Learning, Pr\u00eamio Turing 2018, criador do backpropagation e das Deep Belief Networks and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

geokeo-automation

ComposioHQ/awesome-claude-skills

"Automate Geokeo tasks via Rube MCP (Composio). Always search tools first for current schemas."

geomaster

K-Dense-AI/scientific-agent-skills

Comprehensive geospatial science skill covering remote sensing, GIS, spatial analysis, machine learning for earth observation, and 30+ scientific domains. Supports satellite imagery processing (Sentinel, Landsat, MODIS, SAR, hyperspectral), vector and raster data operations, spatial statistics, point cloud processing, network analysis, cloud-native workflows (STAC, COG, Planetary Computer), and 8 programming languages (Python, R, Julia, JavaScript, C++, Java, Go, Rust) with 500+ code examples. Use for remote sensing workflows, GIS analysis, spatial ML, Earth observation data processing, terrain analysis, hydrological modeling, marine spatial analysis, atmospheric science, and any geospatial computation task.

geometric

bergside/awesome-design-skills

Geometric, structured design with clean typography, neutral colors, precise shapes, and intuitive layouts that stay out of the way.

geometric-intuition

Tibsfox/gsd-skill-creator

Spatial reasoning, coordinate geometry, transformations, and trigonometry for geometric problem solving. Covers Euclidean geometry (points, lines, angles, congruence, similarity), triangle geometry (Pythagorean theorem, laws of sines and cosines), circle geometry (tangent lines, inscribed angles, power of a point), coordinate geometry (distance, midpoint, slope, conic sections), transformations as functions (rotation, reflection, translation, dilation), trigonometry (unit circle, identities, inverse functions), and geometric proof techniques. Use when reasoning about shapes, angles, spatial relationships, coordinate problems, or trigonometric computations.

geometric-layout-repair

elizaOS/eliza

Use when producing a minimally changed repaired 2D layout in JSON from extracted architectural geometry and rule-based clearance constraints.

geometric-volume-calculation

InternScience/scp

Calculate volumes of geometric shapes for engineering design and mathematical analysis.

geometry_trigonometry

InternScience/scp

Geometry & Trigonometry Suite - Solve geometry problems: calculate area, height from sine, angle in degrees, and increase factor. Use this skill for mathematics tasks involving calculate area calculate height from length and sine calculate phi deg calculate increase factor. Combines 4 tools from 1 SCP server(s).

geometry-nodes

arjun988/blender-skills

Blender Geometry Nodes for procedural modeling, scatter systems, vegetation, buildings, pipes, cables, and reusable node groups. Use for procedural asset generation and instancing pipelines via MCP.

geopandas

K-Dense-AI/scientific-agent-skills

Python library for working with geospatial vector data including shapefiles, GeoJSON, and GeoPackage files. Use when working with geographic data for spatial analysis, geometric operations, coordinate transformations, spatial joins, overlay operations, choropleth mapping, or any task involving reading/writing/analyzing vector geographic data. Supports PostGIS databases, interactive maps, and integration with matplotlib/folium/cartopy. Use for tasks like buffer analysis, spatial joins between datasets, dissolving boundaries, clipping data, calculating areas/distances, reprojecting coordinate systems, creating maps, or converting between spatial file formats.

geopandas-geospatial

jaechang-hits/SciAgent-Skills

>-

geopolitical-risk

HKUDS/Vibe-Trading

Geopolitical risk analysis: quantify crisis signals, identify precursors, and build event-driven strategies for war, sanctions, and supply disruption scenarios.

geopolitics

Tibsfox/gsd-skill-creator

Spatial dimensions of political power, state sovereignty, territorial conflict, borders, international governance, and critical geopolitics. Covers classical geopolitics (Mackinder, Ratzel, Mahan), critical geopolitics (Said, O Tuathail), state territory and sovereignty, border theory, international organizations and governance, electoral geography, and postcolonial perspectives on power and space. Use when reasoning about territorial disputes, borders, international relations, state power, colonialism and its legacies, or the politics of geographic representation.

geospatial-analysis

elizaOS/eliza

Analyze geospatial data using geopandas with proper coordinate projections. Use when calculating distances between geographic features, performing spatial filtering, or working with plate boundaries and earthquake data.

geospatial-and-cartographic-visualization

openai/plugins

Design geospatial and cartographic visualizations. Use when the user needs help deciding whether to use a map, choosing projections or basemaps, building choropleths or symbol maps, or implementing thematic maps, slippy maps, or geospatial interactions with D3 geo, Leaflet, MapLibre, Mapbox GL JS, Google Maps, OpenLayers, deck.gl, ArcGIS Maps SDK, Azure Maps, HERE Maps, CesiumJS, or related tools.

geospatial-routing-data

elizaOS/eliza

Geospatial routing data handling for depot and station coordinates, route node IDs, internal index mappings, great-circle distance matrices, and route-distance reconstruction. Use when optimization or reporting tasks involve latitude/longitude, station IDs, depots, distance metrics, vehicle routes, or validating travel distance from reported paths.

gerichtsstand-und-rechtswahl-pruefen

Klotzkette/claude-fuer-deutsches-recht

Gerichtsstand und Rechtswahl bei internationalen Handelsstreitigkeiten: Brüssel Ia VO 1215/2012 (Art. 25 Gerichtsstandsklausel, Art. 7 Erfüllungsort), Lugano-Übereinkommen 2007 (EFTA), Schiedsklausel-Wirksamkeit § 1029 ZPO, New Yorker Übereinkommen 1958, ICC/LCIA/DIS, Rom I VO 593/2008, Rom II VO 864/2007, CISG-Anwendungsbereich, Anerkennung Auslandsurteil §328 ZPO. BGH II ZB 35/20, EuGH C-537/23.

germinal

adaptyvbio/protein-design-skills

>

gerrit-commit-message-review

GerritCodeReview/gerrit

Proofreads and suggests structural improvements for Git commit messages to ensure style guide compliance, completeness, and accuracy.

gerrit-frontend-engineering

GerritCodeReview/gerrit

Provides guidance and best practices on Polygerrit UI development, frontend architecture, and TypeScript/JS coding standards in Gerrit.

gerrit-hygiene-operations

GerritCodeReview/gerrit

Provides rules, patterns, and best practices for code hygiene, formatting, downstream plugin dependencies, and release operations in Gerrit.

gerrit-system-logic

GerritCodeReview/gerrit

Provides rules, patterns, and best practices for Gerrit backend system logic, Java APIs, performance, and correctness.

gesamtbewertung-tragfaehigkeit

Klotzkette/claude-fuer-deutsches-recht

Gesamturteil zur Tragfaehigkeit einer Marktabgrenzung: hoch mittel oder gering. Fasst zentrale Schwachstellen in 3 bis 5 scharfen Punkten zusammen. Bewertet Angreifbarkeit vor Gericht oder Behoerde und empfiehlt prozesstaktische Konsequenzen fuer das eigene Team.

gesamtnoten-aggregation

Klotzkette/claude-fuer-deutsches-recht

Aggregiert Einzelbewertungen aus Leistungs-, Verhaltens- und Schlussformel-Analyse zur Gesamtnote. Berücksichtigt unterschiedliche Gewichtung der Zeugnisbereiche und gibt eine begründete Gesamtnotenspanne aus.

geschaeftsfuehrer-haftung-43-gmbhg

Klotzkette/claude-fuer-deutsches-recht

Pruefraster fuer die Geschaeftsfuehrer-Haftung nach 43 GmbHG iVm 93 AktG. Sorgfalt ordentlicher Geschaeftsmann Business Judgement Rule analoge Anwendung 93 Abs. 1 Satz 2 AktG fuer GmbH BGH II ZR 124/06 ARAG/Garmenbeck. Insolvenzantragspflicht-Verletzung 15a InsO Zahlungsverbot 15b InsO Compliance-Pflichten Steuer-Haftung 69 AO Sozialversicherung 266a StGB. Entlastung Sperrwirkung Beweislast Verjaehrung fuenf Jahre 43 Abs. 4 GmbHG. D&O-Versicherung Selbstbehalt.

geschgehg-bausteine

Klotzkette/claude-fuer-deutsches-recht

Bausteine zum Geschäftsgeheimnisschutzgesetz für KI-Nutzungsrichtlinien: § 1 Abs. 3 Nr. 1 GeschGehG, angemessene Geheimhaltungsmaßnahmen beim KI-Einsatz, Verhältnis zu § 203 StGB und §§ 43a, 43e BRAO.

gesellschafterbeschluss

Klotzkette/claude-fuer-deutsches-recht

Erstellung, Pruefung und Anfechtung von Gesellschafterbeschluessen in GmbH (47 und 48 GmbHG) und AG (133 ff. AktG); Mehrheitserfordernisse, Beschlussfaehigkeit, Formfragen, Protokollfuehrung sowie Nichtigkeit (241 AktG analog) und Anfechtbarkeit (246 AktG analog). Laedt bei Mandaten zur Beschlussfassung, Anfechtungsklage oder Nichtigkeitsfeststellung.

gesellschafterbeschluss-kapitalerhoehung

Klotzkette/claude-fuer-deutsches-recht

Beschluss-Entwurf Erhoehung des Stammkapitals um den Nennbetrag der neuen Anteile gegen Sacheinlage (Forderung aus Wandeldarlehen), Ausschluss Bezugsrechte der Altgesellschafterinnen, Zulassung Lender als neuer Gesellschafter, notarielle Beurkundung § 53 Abs. 2 GmbHG, Sacheinlagebericht.

gesellschafterbeschluss-vorbereiten

Klotzkette/claude-fuer-deutsches-recht

Gesellschafterbeschluss-Entwurf zur Bestaetigung der Vertragsunterzeichnung und zur grundsaetzlichen Bereitschaft der Kapitalerhoehung im Wandlungsfall. Einberufungsmodalitaeten, Ladungsfristen nach § 51 GmbHG (mindestens eine Woche) und Verzichtsmoeglichkeit nach § 51 Abs. 3 GmbHG fuer einstimmige Beschlussfassung.

gesellschafterdarlehen-rangruecktritt

Klotzkette/claude-fuer-deutsches-recht

Erzeugt eine Erklaerung zum qualifizierten Rangruecktritt fuer Gesellschafterdarlehen nach § 19 Abs. 2 S. 2 InsO. BGH-konforme Formulierung BGH II ZR 18/19 — der Rangruecktritt muss sich erstrecken auf Insolvenz Glaeubiger Geschaeftsbeendigung und Liquidation. Effekt im insolvenzrechtlichen Status die Forderung wird nicht passiviert. Form schriftlich beidseitig unterzeichnet — notarielle Beurkundung empfohlen. Verbunden mit Pflicht zur Anzeige beim Finanzamt wegen steuerlichen Folgen.

gesellschafterliste-aktualisieren

Klotzkette/claude-fuer-deutsches-recht

Aktualisierte Gesellschafterliste nach § 40 GmbHG mit fortlaufenden Nummern, neuem Lender-Eintrag nach Kapitalerhoehung, Bestaetigung Geschaeftsfuehrung, Notar-Bestaetigung. Gutglaubenswirkung nach § 16 GmbHG und Frist zur Einreichung beim Handelsregister. Transparenzregister-Meldepflicht § 19 GwG.

gesellschafterstreit-loesungsstrategie

Klotzkette/claude-fuer-deutsches-recht

Strategie bei Gesellschafterstreit insbesondere GmbH-Two-Tier-Konflikten. Mediation Gespraechskonzept Beschluss-Anfechtungsklage 246 AktG analog Abberufungs-Klage Geschaeftsfuehrer 38 GmbHG Hinauskuendigungs-Verfahren Anteilseinziehung 34 GmbHG Ausschluss-Klage 140 HGB analog. Praxisorientierte Verhandlungsstrategie Wertbestimmungs-Verfahren Abfindungsberechnung BGH Verkehrswert nicht Buchwert. Schiedsklausel-Pruefung DIS-Schiedsgerichtsordnung.

gesellschafterversammlung-einberufen

Klotzkette/claude-fuer-deutsches-recht

Einberufung der ausserordentlichen Gesellschafterversammlung mit Tagesordnung Kapitalerhoehung gegen Sacheinlage (Wandlung Wandeldarlehen). Ladungsfristen nach § 51 GmbHG (mindestens eine Woche), Moeglichkeit des Ladungsfristverzichts nach § 51 Abs. 3 GmbHG, Tagesordnungspflichten, Vollmachtsregelung.

gesellschafts-compliance

Klotzkette/claude-fuer-deutsches-recht

Gesellschafts-Compliance-Tracker – Initialisierung, Fälligkeitsbericht, Status-Update, Gesundheits-Audit, Export. Pflegt eine compliance-tracker.yaml aus der Gesellschaftstabelle, berechnet Einreichungsfristen nach Rechtsträger und Rechtsordnung und zeigt auf, was in den nächsten 30/60/90 Tagen fällig ist. Trigger: „Gesellschafts-Compliance\", „Einreichungsfristen\", „Bilanzpublizität\", „Transparenzregister\", „Jahresabschluss einreichen\", „was ist fällig\".

gesellschaftsgruender-beirat-advisory-board

Klotzkette/claude-fuer-deutsches-recht

Beirat Advisory Board Aufsichtsrat. Beiratsordnung Aufgaben Besetzung Verguetung. Pflicht vs freiwillig. Bei GmbH typisch freiwillig Empfehlung bei Mittelstand und Family Office. Beispiel-Klausel Satzung Beiratsordnung Tagesordnung Beirat-Meeting. Streit-Schlichtungs-Funktion. Paragraf 52 GmbHG analog AktG Vorschriften. Haftung D-und-O-Versicherung.