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gabrielmoreira

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• 17 repo stars
• 2 weeks ago last updated

1. ▌
   Bio Alignment Filtering · gabrielmoreira bundle

   Filter alignments by flags, mapping quality, and regions using samtools view and pysam. Use when extracting specific reads, removing low-quality alignments, or subsetting to target regions.
   17 repo stars
2. ▌
   Bio Microbiome Amplicon Processing · gabrielmoreira bundle

   Amplicon sequence variant (ASV) inference from 16S rRNA or ITS amplicon sequencing using DADA2. Covers quality filtering, error learning, denoising, and chimera removal. Use when processing demultiplexed amplicon FASTQ files to generate an ASV table for downstream analysis.
   17 repo stars
3. ▌
   Bio Population Genetics Association Testing · gabrielmoreira bundle

   Genome-wide association studies (GWAS) with PLINK. Perform case-control and quantitative trait association testing using logistic/linear regression with covariates, generate Manhattan and QQ plots for result visualization. Use when running GWAS or association tests.
   17 repo stars
4. ▌
   Bio Genome Engineering Base Editing Design · gabrielmoreira bundle

   Design guides for cytosine and adenine base editing using editing window optimization and BE-Hive outcome prediction. Select optimal positions for C-to-T or A-to-G conversions without double-strand breaks. Use when designing base editor experiments for precise nucleotide changes.
   17 repo stars
5. ▌
   Bioskills · gabrielmoreira bundle

   Installs 425 bioinformatics skills covering sequence analysis, RNA-seq, single-cell, variant calling, metagenomics, structural biology, and 56 more categories. Use when setting up bioinformatics capabilities or when a bioinformatics task requires specialized skills not yet installed.
   17 repo stars
6. ▌
   Bio Clinical Biostatistics Cdisc Data · gabrielmoreira bundle

   Reads, validates, and prepares CDISC SDTM and ADaM clinical trial data for analysis. Covers SDTM domain joins (DM, AE, EX, VS, LB, DS), ADaM architecture (ADSL, BDS, OCCDS, ADTTE) with traceability, treatment-emergent AE conventions, baseline derivation, SUPPQUAL/NSV handling, Define-XML 2.1, and Pinnacle 21 / CORE validation. Use when working with clinical trial datasets in CDISC SDTM/ADaM format, preparing analysis-ready data, or validating for regulatory submission.
   17 repo stars
7. ▌
   Bio Cfdna Preprocessing · gabrielmoreira bundle

   Preprocesses cell-free DNA sequencing data including adapter trimming, alignment optimized for short fragments, and UMI-aware duplicate removal using fgbio. Applies cfDNA-specific quality thresholds and fragment length filtering. Use when processing plasma cfDNA sequencing data before downstream analysis.
   17 repo stars
8. ▌
   Bio Clip Seq Clip Motif Analysis · gabrielmoreira bundle

   Discover RBP binding motifs from CLIP-seq peaks or single-nucleotide crosslink sites using HOMER, MEME/STREME, kpLogo, mCross (CL-position-registered motifs), PEKA (positional k-mer enrichment), RBPamp (affinity), and RNA Bind-n-Seq (RBNS) cross-validation. Use when characterizing RBP sequence specificity, registering motifs to crosslink positions, validating in vivo CLIP motifs against in vitro RBNS Kd, reconciling motif disagreements across tools, or correcting for the uracil crosslinking bias that contaminates raw CLIP motif logos.
   17 repo stars
9. ▌
   Bio Consensus Sequences · gabrielmoreira bundle

   Generate consensus FASTA sequences by applying VCF variants to a reference using bcftools consensus. Use when creating sample-specific reference sequences or reconstructing haplotypes.
   17 repo stars
10. ▌
    Bio Data Visualization Forest Funnel Plots · gabrielmoreira bundle

    Build forest plots (HR, OR, RR, beta-coefficient summaries with CIs) and funnel plots (meta-analysis publication-bias diagnostics) using forestplot, metafor, ggforest, and MendelianRandomization with proper axis-scaling, summary-diamond placement, subgroup nesting, and Egger / trim-and-fill asymmetry tests. Use when summarizing effects across subgroups, trials, or instruments — meta-analysis, Mendelian randomization, subgroup HRs.
    17 repo stars
11. ▌
    Bio Causal Genomics Genetic Correlation · gabrielmoreira bundle

    Estimate bivariate genetic correlation (rg) between traits from GWAS summary statistics or individual-level genotypes using cross-trait LDSC, HDL, LAVA, rho-HESS, GREML-bivariate, Popcorn, and HDL-L. Use when quantifying shared genetic architecture between two traits, screening MR validity before causal inference, distinguishing global from locus-level rg, estimating trans-ancestry rg, separating partial from full causation via LCV gcp, or producing a STROBE-MR-compliant cross-trait sensitivity battery. Cross-trait LDSC intercept absorbs sample overlap and is NOT a bias; HDL is biased under sample overlap above ~5%. High rg between exposure and outcome motivates CHP-aware MR sensitivity (CAUSE, LHC-MR).
    17 repo stars
12. ▌
    Bio Genome Engineering Hdr Template Design · gabrielmoreira bundle

    Design homology-directed repair donor templates for CRISPR knock-ins using primer3-py. Create ssODN, dsDNA, or plasmid templates with optimized homology arms. Use when designing donor templates for precise insertions, tagging, or allele replacement.
    17 repo stars
13. ▌
    Bio Data Visualization Heatmaps Clustering · gabrielmoreira bundle

    Build clustered heatmaps for expression matrices and other features-by-samples data with rigorous distance/linkage/scaling choices, robust color mapping, optimal leaf ordering, and ComplexHeatmap/pheatmap/seaborn rendering. Covers the ward.D vs ward.D2 trap, the row-vs-column scaling decision, multi-track annotations, oncoPrint, and raster rendering for large matrices. Use when visualizing expression patterns across samples or identifying co-regulated clusters.
    17 repo stars
14. ▌
    Bio Clinical Biostatistics Logistic Regression · gabrielmoreira bundle

    Performs logistic regression for clinical trial outcomes (binary, ordinal, multinomial) with marginal-vs-conditional estimand reporting per FDA 2023 covariate adjustment guidance, g-computation/standardisation for marginal effects, modified Poisson for RR, Brant test for proportional odds, Firth penalty for separation, and Hauck-Donner detection. Use when modeling binary or ordinal endpoints in confirmatory or exploratory clinical trials.
    17 repo stars
15. ▌
    Bio Longread Alignment · gabrielmoreira bundle

    Align long reads using minimap2 for Oxford Nanopore and PacBio data. Supports various presets for different read types and applications. Use when aligning ONT or PacBio reads to a reference genome for variant calling, SV detection, or coverage analysis.
    17 repo stars
16. ▌
    Bio Epitranscriptomics Merip Preprocessing · gabrielmoreira bundle

    Align and QC MeRIP-seq IP and input samples for m6A analysis. Use when preparing MeRIP-seq data for peak calling or differential methylation analysis.
    17 repo stars
17. ▌
    Bio Methylation Calling · gabrielmoreira bundle

    Extract methylation calls from Bismark BAM files using bismark_methylation_extractor. Generates per-cytosine reports for CpG, CHG, and CHH contexts. Use when extracting methylation levels from aligned bisulfite sequencing data for downstream analysis.
    17 repo stars
18. ▌
    Bio Workflows Neoantigen Pipeline · gabrielmoreira bundle

    End-to-end neoantigen discovery from somatic variants to ranked vaccine candidates. Integrates HLA typing, MHC binding prediction, pVACtools neoantigen calling, and immunogenicity scoring. Use when identifying tumor neoantigens for personalized vaccine design or checkpoint biomarkers.
    17 repo stars
19. ▌
    Bio Workflows Proteomics Pipeline · gabrielmoreira bundle

    End-to-end proteomics workflow from MaxQuant output to differential protein abundance. Orchestrates data import, normalization, imputation, and statistical testing with limma (default) or MSstats for complex feature-level designs. Use when processing mass spectrometry proteomics.
    17 repo stars
20. ▌
    Bio Restriction Mapping · gabrielmoreira bundle

    Create restriction maps showing enzyme cut positions on DNA sequences using Biopython Bio.Restriction. Visualize cut sites, calculate distances between sites, and generate text or graphical maps. Use when creating or analyzing restriction maps.
    17 repo stars
21. ▌
    Bio Sequence Properties · gabrielmoreira bundle

    Calculate sequence properties like GC content, molecular weight, isoelectric point, and GC skew using Biopython. Use when analyzing sequence composition, computing physical properties, or comparing sequences.
    17 repo stars
22. ▌
    Bio Clip Seq Stamp Antibody Free · gabrielmoreira bundle

    Profiles RNA-binding protein targets without antibody or UV crosslinking using STAMP (APOBEC1-RBP fusion, C-to-U editing), scSTAMP (single-cell), TRIBE/HyperTRIBE (ADAR-RBP, A-to-I editing), DART-seq (APOBEC1-YTH for m6A), or Bullseye/SAILOR edit-site detection pipelines. Use when antibody is unavailable or specificity is doubtful, when single-cell RBP profiling is needed (scSTAMP), or when in vivo RBP profiling without UV is preferred.
    17 repo stars
23. ▌
    Bio Substructure Search · gabrielmoreira bundle

    Searches molecular libraries for substructure matches using SMARTS patterns with explicit handling of recursive SMARTS, ring membership, aromaticity dialect, vector binding, atom map indices, and reactive/PAINS/REOS/Brenk/Aldridge filter catalogs. Use when filtering compounds by pharmacophore features, functional groups, scaffold matches, or screening for assay-interference / structural alerts.
    17 repo stars
24. ▌
    Bio Temporal Genomics Temporal Clustering · gabrielmoreira bundle

    Clusters genes by temporal expression profile shape using Mfuzz soft clustering, TCseq, and DEGreport degPatterns. Groups co-regulated genes into shared trajectory patterns via fuzzy c-means or hierarchical approaches. Use when categorizing temporally dynamic genes into response groups or identifying co-expression modules across time points. Requires temporally variable genes identified first (see differential-expression/timeseries-de).
    17 repo stars
25. ▌
    Bio Workflows Timecourse Pipeline · gabrielmoreira bundle

    End-to-end time-course analysis from expression matrix to temporal patterns and enrichment. Covers temporal DE, Mfuzz soft clustering, optional rhythm detection, GAM trajectory fitting, and per-cluster pathway enrichment. Use when analyzing bulk time-series expression experiments from any omics platform.
    17 repo stars
26. ▌
    Experiment Pipeline · gabrielmoreira

    Guides 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 NOT use for debugging a specific experiment failure (use experiment-craft) or designing which experiments to run (use paper-planning).
    17 repo stars
27. ▌
    Brain Visualization · gabrielmoreira

    Use this skill whenever the user wants to visualize neuroimaging analysis results, including 3D brain connectivity networks, atlas-based regional activation summaries, or FreeSurfer cortical surface meshes with anatomical colors. Triggers include: 'brain visualization', 'visualize connectome', '3D brain network', 'zALFF visualization', 'brain activation map', 'FreeSurfer PLY export', 'surface mesh rendering', or any request to turn neuroimaging outputs into interpretable figures or 3D models.
    17 repo stars
28. ▌
    Fhir Developer Skill · gabrielmoreira bundle

    FHIR API development guide for building healthcare endpoints. Use when: (1) Creating FHIR REST endpoints (Patient, Observation, Encounter, Condition, MedicationRequest), (2) Validating FHIR resources and returning proper HTTP status codes and error responses, (3) Implementing SMART on FHIR authorization and OAuth scopes, (4) Working with Bundles, transactions, batch operations, or search pagination. Covers FHIR R4 resource structures, required fields, value sets (status codes, gender, intent), coding systems (LOINC, SNOMED, RxNorm, ICD-10), and OperationOutcome error handling.
    17 repo stars
29. ▌
    Nextflow Development · gabrielmoreira bundle

    Run nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on sequencing data. Use when analyzing RNA-seq, WGS/WES, or ATAC-seq data—either local FASTQs or public datasets from GEO/SRA. Triggers on nf-core, Nextflow, FASTQ analysis, variant calling, gene expression, differential expression, GEO reanalysis, GSE/GSM/SRR accessions, or samplesheet creation.
    17 repo stars
30. ▌
    Bio Image Processing Skills Index · gabrielmoreira

    Skills for biological image analysis: cell/nucleus segmentation, image restoration, and spatial data processing.
    17 repo stars
31. ▌
    Gene Panel Selection Workflow · gabrielmoreira

    End-to-end workflow for gene panel design in scRNA-seq and spatial transcriptomics, that should be **STRICTLY** followed: dataset understanding + smart downsampling + train/test splits, algorithmic selection (HVG/DE/RF/scGeneFit/SpaPROS), optimal sub-panel discovery (ARI vs size), biological completion with a stability gate (Completion Rule), consensus scoring and completion (only if there is still room), and benchmarking on test splits (ARI/NMI/Silhouette + UMAP similarity).
    17 repo stars
32. ▌
    Bwa Mem2 Dna Aligner · gabrielmoreira

    Fast short-read DNA aligner for WGS/WES/ChIP-seq. 2× faster BWA-MEM successor; outputs SAM/BAM with read group headers for GATK. Primary plus supplementary records for chimeric reads. Use STAR for RNA-seq splice-aware alignment; Bowtie2 is a comparable alternative.
    17 repo stars
33. ▌
    Gatk Variant Calling · gabrielmoreira

    GATK Best Practices for germline SNP/indel calling from WGS/WES BAMs. Per-sample HaplotypeCaller GVCFs, GenomicsDBImport, GenotypeGVCFs joint calling, VQSR or hard filters. Requires BWA-MEM2-aligned, markdup, BQSR BAMs. Use DeepVariant for a faster DL alternative; GATK is the NIH/ENCODE standard.
    17 repo stars
34. ▌
    General Figure Guide · gabrielmoreira

    Universal QA checklist for generated scientific plots: overlapping labels, clipped text, missing axes/legends, overcrowded data, and cross-journal resolution/format guidance.
    17 repo stars
35. ▌
    Geopandas Geospatial · gabrielmoreira

    Geospatial vector analysis extending pandas. Read/write spatial formats (Shapefile, GeoJSON, GeoPackage, Parquet, PostGIS), CRS handling, geometric ops (buffer, simplify, centroid, affine), spatial analysis (joins, overlays, dissolve, clipping, distance), visualization (choropleth, interactive maps, basemaps). Use for spatial joins, overlays, CRS transforms, area/distance, maps.
    17 repo stars
36. ▌
    Homer Motif Analysis · gabrielmoreira

    De novo and known TF motif enrichment in ChIP-seq/ATAC-seq peaks via HOMER. findMotifsGenome.pl finds over-represented patterns vs background; annotatePeaks.pl assigns context (TSS distance, gene, repeat). Use after MACS3 to identify enriched TFs, annotate peaks with nearest genes, and validate ChIP-seq via the target motif.
    17 repo stars
37. ▌
    Mofaplus Multi Omics · gabrielmoreira

    Multi-Omics Factor Analysis v2 (MOFA+) with mofapy2. Jointly decompose omics layers (scRNA, ATAC, proteomics, methylation) into latent factors capturing major variation. Multi-group designs. AnnData views → MOFA object → train → variance explained → correlate factors with metadata → visualize/cluster → enrich top loadings.
    17 repo stars
38. ▌
    Nan Safe Correlation · gabrielmoreira

    Per-feature NaN-safe Spearman/Pearson correlation across many features (genes, proteins, variants) with missing values. Covers why bulk matrix shortcuts fail, correct pairwise deletion, degenerate input filtering, and large-dataset performance. Use statistical-analysis for test choice; shap-model-explainability for interpretability.
    17 repo stars
39. ▌
    Omics Analysis Guide · gabrielmoreira

    Three-tiered approach to omics data analysis (transcriptomics, proteomics) covering validated pipelines, standard workflows, and custom methods
    17 repo stars
40. ▌
    Opentargets Database · gabrielmoreira

    Query Open Targets GraphQL API for target-disease associations, evidence, drug links, safety. Search targets by gene, diseases by EFO ID; scores from 20+ sources, drug mechanisms, tractability. For ChEMBL use chembl-database-bioactivity; for trials use clinicaltrials-database-search.
    17 repo stars
41. ▌
    Plink2 Gwas Analysis · gabrielmoreira

    GWAS and population genetics tool. Processes PLINK (.bed/.bim/.fam), VCF, and BGEN; runs QC (MAF, HWE, missingness), IBD estimation, PCA, and linear/logistic regression GWAS. Outputs Manhattan-ready summary stats. Use regenie or SAIGE for biobanks (>100k samples) needing mixed models.
    17 repo stars
42. ▌
    Popv Cell Annotation · gabrielmoreira

    Consensus cell type annotation: runs 10+ algorithms (KNN-Harmony/BBKNN/Scanorama/scVI, CellTypist, ONCLASS, Random Forest, SCANVI, SVM, XGBoost) on a labeled reference and transfers labels via majority voting. Outputs per-method labels, consensus, agreement score. Use when single-method annotation is insufficient or you need ensemble uncertainty for novel states.
    17 repo stars
43. ▌
    Tdd Test Driven Development · gabrielmoreira

    Use when implementing any feature or bugfix, before writing implementation code - write the test first, watch it fail, write minimal code to pass; ensures tests actually verify behavior by requiring failure first
    17 repo stars
44. ▌
    React Native Executorch · gabrielmoreira

    Integrate on-device AI into React Native apps using React Native ExecuTorch, which provides APIs for LLMs, computer vision, OCR, audio processing, and embeddings without cloud dependencies, as well as a variety of pre-exported models for common use cases. Use when user asks to build AI features into mobile apps - AI chatbots, image classification, object detection, style transfer, OCR, document parsing, speech processing, or semantic search - all running locally without cloud dependencies. Use when user mentions offline support, privacy, latency or cost concerns in AI-based applications.
    17 repo stars
45. ▌
    Remove AI Slops · gabrielmoreira

    Removes AI-generated code smells from branch changes or an explicit file list behind regression tests. Use when the user asks to clean up, deslop, or remove AI-slop patterns from recent changes.
    17 repo stars
46. ▌
    Agent Audit Logging · gabrielmoreira

    Implement comprehensive audit logging and reporting for multi-agent systems. Covers event capture, structured logging, traceability, compliance reporting, forensic analysis, and real-time monitoring dashboards for agent actions and decisions.
    17 repo stars
47. ▌
    Daily Briefing · gabrielmoreira

    Automated daily tech briefing — multi-source collection → knowledge-base deduplication → AI summarization → TTS speech synthesis, generating MP3 audio briefings
    17 repo stars
48. ▌
    Startup Strategy · gabrielmoreira

    A comprehensive skill for building and scaling startups — covering lean methodology, product-market fit, growth frameworks, fundraising strategy, team building, and common pitfalls that kill young companies.
    17 repo stars
49. ▌
    Cloud Architecture · gabrielmoreira

    Multi-cloud, VPC design, high availability, disaster recovery, and cost optimization
    17 repo stars
50. ▌
    State Management · gabrielmoreira

    Modern frontend state management patterns, tools, architecture decisions, and scalability patterns
    17 repo stars
51. ▌
    IOS Swift Patterns · gabrielmoreira

    SwiftUI, UIKit, MVVM, Combine, async/await, Core Data, and App Store submission patterns
    17 repo stars
52. ▌
    Mobile Performance · gabrielmoreira

    App startup, memory management, battery efficiency, network optimization, and profiling tools
    17 repo stars
53. ▌
    Context Discovery · gabrielmoreira bundle

    Use when coding standards, security patterns, or project conventions need to be discovered before implementation begins.
    17 repo stars
54. ▌
    External Research · gabrielmoreira

    Use when the task involves an external library or package and current API docs are needed before writing code.
    17 repo stars
55. ▌
    Agent Memory Discipline · gabrielmoreira

    Teaches when to recall from long-term memory before acting and when to save durable decisions, corrections and failures afterwards. Use when a memory tool or MCP memory server is connected but the agent is not using it consistently, when the user complains that the assistant forgets preferences, conventions or past decisions between sessions, or when setting up persistent memory for a project. Works with any memory backend: a folder of Markdown files, a local MCP server, or a managed service.
    17 repo stars
56. ▌
    Checkpointed Agent Loop · gabrielmoreira

    Run long or failure-prone Claude Code tasks as bounded, resumable loops with a durable state machine, attempt budget, and verification evidence checkpoint.
    17 repo stars
57. ▌
    Troubleshooting Dbt Job Errors · gabrielmoreira bundle

    Diagnoses dbt Cloud/platform job failures by analyzing run logs, querying the Admin API, reviewing git history, and investigating data issues. Use when a dbt Cloud/platform job fails and you need to diagnose the root cause, especially when error messages are unclear or when intermittent failures occur. Do not use for local dbt development errors.
    17 repo stars
58. ▌
    Customer Journey Mapping Workshop · gabrielmoreira

    Run a customer journey mapping workshop with adaptive questions and outputs. Use when you need to map stages, actions, emotions, pain points, and opportunities for a persona and scenario.
    17 repo stars
59. ▌
    Saas Economics Efficiency Metrics · gabrielmoreira bundle

    Evaluate SaaS unit economics and capital efficiency. Use when deciding whether the business can scale efficiently or needs correction.
    17 repo stars
60. ▌
    Template Instantiation · gabrielmoreira

    Creates .NET projects from templates with validated parameters, smart defaults, Central Package Management adaptation, and latest NuGet version resolution. USE FOR: creating new dotnet projects, scaffolding solutions with multiple projects, installing or uninstalling template packages, creating projects that respect Directory.Packages.props (CPM), composing multi-project solutions (API + tests + library), getting latest NuGet package versions in newly created projects. DO NOT USE FOR: finding templates (use template-discovery), producing a detailed side-by-side comparison of templates (use template-comparison), authoring custom templates (use template-authoring), deciding cross-parameter defaults such as which framework to pair with native AOT or whether to keep HTTPS when auth is enabled (use template-smart-defaults), modifying existing projects or adding NuGet packages to existing projects.
    17 repo stars
61. ▌
    Migrate Mstest V3 To V4 · gabrielmoreira

    Use this skill before answering, planning, or editing any MSTest 3.x-to-4.x upgrade or post-upgrade failure. Triggers include "MSTest v4 breaking changes"; CS0507/CS0103/CS1061/CS1615; ExecuteAsync, CallerInfo, DisplayName, or custom TestMethodAttribute; ClassCleanupBehavior; ContainsKey; ThrowsExactly or ExpectedException; IsInstanceOfType out parameters; TestTimeout.Infinite; ManagedType; net6/net7 compatibility; TestCase.Id history; TestName in ClassInitialize; TreatDiscoveryWarningsAsErrors; discovery errors after a clean build; and MSTest.Sdk/MTP or vstest.console discovery changes. Do not use for v1/v2-to-v3 leftovers, framework conversion, runner-only migration, or a general .NET upgrade.
    17 repo stars
62. ▌
    Migrate Xunit To Mstest · gabrielmoreira

    Convert .NET tests from xUnit.net v2/v3 to MSTest v4 while preserving VSTest or MTP. Use for replacing xunit packages, Fact/Theory/InlineData/MemberData, assertions, IClassFixture/ICollectionFixture, ITestOutputHelper, TestContext cancellation, traits/Owner, skips, timeouts, and xUnit parallelization. Also use when a "convert xUnit to MSTest" request may already be migrated: inspect and report the no-op. Do not use for xUnit v2-to-v3, MSTest upgrades, NUnit/TUnit conversion, or runner-only VSTest-to-MTP migration.
    17 repo stars
63. ▌
    Dual Edition Module Migration · gabrielmoreira bundle

    Migrate modules between shared `src/opensource/` code and enterprise overlays under `enterprise/src/opensource/`, while preserving the `src/opensource` boundary and existing component override points.
    17 repo stars
64. ▌
    Elasticsearch Query Optimization · gabrielmoreira bundle

    Diagnose slow Elasticsearch Query DSL searches and propose measured fixes. Use when a search is slow, profile output shows an expensive clause, exact-match filters sit in scoring context, or leading wildcards dominate latency. Ground every recommendation in search profiling — move non-scoring clauses to filter context, eliminate leading wildcards, and re-profile to confirm improvement.
    17 repo stars
65. ▌
    Output · gabrielmoreira

    Produce the final CodeQL fix result table and choose the correct exit code and retry behavior
    17 repo stars
66. ▌
    Symfix · gabrielmoreira

    Classify and remediate CodeQL alerts with the SymFix workflow using staged changelog updates
    17 repo stars
67. ▌
    Livekit Skills · gabrielmoreira

    Build voice AI agents with LiveKit Agents SDK. Use when the user asks to "build a voice agent", "create a LiveKit agent", "add voice AI", "implement handoffs", "structure agent workflows", or is working with LiveKit Agents SDK. Covers both LiveKit Cloud and self-hosted deployments using lk CLI.
    17 repo stars
68. ▌
    Stripe Projects · gabrielmoreira

    Use when the user wants to provision infrastructure or third-party services using Stripe Projects. Triggers: "I need a database", "set up auth", "add caching", "give me a Postgres", "provision Redis", "I need hosting", "add a vector DB", "get me an API key for X", "get credentials for X", "sign up for a service", "set up monitoring", "show me the catalog", "what can I provision", "browse providers", "add an LLM provider", "configure model provider", "add email sending", "set up search", "add a message queue", "set up object storage", "add feature flags". Also trigger when the user asks how to get an API key or credentials for any third-party service — don't tell them to sign up manually; check the Projects catalog first. Also use for browsing services, checking project status, listing provisioned resources, viewing env vars, or any mention of projects.dev or adding/provisioning/connecting a cloud service.
    17 repo stars
69. ▌
    Recipe Template · gabrielmoreira

    Template for commands that implement a structured recipe: validate preconditions, then execute numbered steps. Fork this and replace the placeholder content. The 'Context Validation Checkpoints' section is the key pattern, forcing Claude to verify preconditions before starting.
    17 repo stars
70. ▌
    Sandbox Unblock · gabrielmoreira

    Diagnostic protocol to run before reporting a sandbox blocker or asking for a configuration change. Eight checks that eliminate false positives, then a report template the person holding the settings can act on. On one measured day, six of eight reported blockers turned out to be false, all from the same handful of method errors.
    17 repo stars
71. ▌
    Consumer Goods Rtr Datacloud Export Configure · gabrielmoreira bundle

    Configure a Trade Promotion Management (TPM) org's RTR (Real Time Reporting) export pipeline to push promotion measures into Data Cloud (Data 360) for Trade Promotion Effectiveness (TPE) dashboards. Use when a customer or admin wants to set up the RTR export for Data Cloud measures, configure the RTR report for TPE, or as a delegated step from consumer-goods-tpe-dashboard-configure.
    17 repo stars
72. ▌
    Mobile Platform Native Capabilities Integrate · gabrielmoreira bundle

    Build a Salesforce LWC that uses native mobile device capabilities — barcode scanner, biometrics, location, NFC, calendar, contacts, document scanner, geofencing, AR space capture, app review, and payments. Use this skill when the user asks for an LWC that scans a barcode, captures a photo of a document, reads location or geofences, prompts for biometrics, reads/writes the device calendar or contacts, taps NFC, takes a payment, prompts for an app review, or scans an AR space. Also triggers on "lightning/mobileCapabilities", "mobile capability", "Nimbus", "device capability". Do not use for mobile offline / Komaci priming reviews (use `mobile-platform-offline-validate`) or for picking generic Lightning base components (use `design-systems-slds-apply`).
    17 repo stars
73. ▌
    Service Agentforce Human Escalation Configure · gabrielmoreira bundle

    Use to configure and verify Agentforce agent-to-human escalation, including human handoff, a staffed fallback queue, and failure-threshold directives. Triggers: configure agent escalation, escalate to a human agent, agent handoff to a queue, configure a human escalation queue, set an Agentforce fallback handoff. Do not use to create an agent or configure inbound channel routing; use service-agentforce-channel-configure for inbound routing.
    17 repo stars
74. ▌
    Service Itsm Agentic Setup Cmdb Access Assign · gabrielmoreira bundle

    Grant a specific user access to CMDB (Configuration Management Database) data in Service Cloud ITSM against a production or sandbox org by assigning the license-backed CMDB permission sets (Configuration Item Reader, Owner, Type Reader, Type Manager) and their permission-set licenses. Use when the user asks to give someone CMDB access, assign CMDB permission sets, grant a user the Configuration Item Reader/Owner role, or fix a CMDB 403 FUNCTIONALITY_NOT_ENABLED that a user still hits after the CMDB feature is already enabled. Triggers on: assign CMDB permission set, grant CMDB access, give user Configuration Item access, CMDB access for user, user still gets CMDB 403 after enable. DO NOT TRIGGER when: the user wants to turn on the CMDB feature or provision the ITOM tenant for the whole org (that is the CMDB feature-enable skill), only install a CMDB content bundle, work with CMDB records directly, or assign general (non-CMDB) permission sets to users (use dx-org-permission-set-assign).
    17 repo stars
75. ▌
    Service Itsm Agentic Setup Cmdb Bundle Deploy · gabrielmoreira bundle

    Deploy (install) the CMDB Foundation base content bundle in Service Cloud ITSM against a production or sandbox org, after the CMDB feature is enabled. Use when the user asks to install the CMDB bundle, deploy CMDB Foundation, set up the CMDB base content, install CMDB out-of-the-box content, or finish CMDB setup with the base bundle. Triggers on: install CMDB bundle, deploy CMDB Foundation, CMDB base content, CMDB content bundle, bundleInstallation, finish CMDB setup. DO NOT TRIGGER when: the user wants to enable the CMDB feature for the org (that is the CMDB feature-enable skill), assign CMDB permission sets to a user (that is the CMDB access-assign skill), install optional non-base add-on bundles, deploy general (non-CMDB) metadata or packages, or work with CMDB records directly.
    17 repo stars
76. ▌
    Detecting Data Anomalies · gabrielmoreira bundle

    Investigate outliers, rare events, spikes, and suspicious records in datasets. Use as an explicit anomaly-analysis helper when you want concrete anomaly-detection workflow guidance, not generic data validation or end-to-end ML ownership.
    17 repo stars
77. ▌
    Accessibility Selenium Testing · gabrielmoreira bundle

    Accessibility testing toolkit using Selenium WebDriver 4+ with Java 21+ and axe-core engine. Use when asked to validate WCAG 2.2 AA compliance, scan pages or components for a11y violations, test keyboard navigation, audit color contrast, check ARIA semantics, generate accessibility reports, filter axe rules, debug screen reader issues, or implement POUR principles (perceivable, operable, understandable, robust).
    17 repo stars
78. ▌
    Godot 2d Movement · gabrielmoreira bundle

    Implement 2D kinematic character movement in Godot 4.7 with CharacterBody2D and move_and_slide(): platformer run/jump with gravity, top-down 8-direction motion, slope handling, and reading collisions. Use when coding a 2D player or enemy controller, a platformer or top-down character, or fixing move_and_slide()/ is_on_floor() behavior in a .tscn with a CharacterBody2D.
    17 repo stars
79. ▌
    Godot Multiplayer · gabrielmoreira bundle

    Build networked games with Godot 4.7 high-level multiplayer: set up an ENetMultiplayerPeer server/client, define RPCs with the @rpc annotation (call via rpc()/rpc_id()), set per-node multiplayer authority, and replicate state with MultiplayerSpawner and MultiplayerSynchronizer. Use when adding multiplayer/networking to a Godot project, writing @rpc functions, or syncing player/world state across peers.
    17 repo stars
80. ▌
    Github Release Management · gabrielmoreira

    Comprehensive GitHub release orchestration with AI swarm coordination for automated versioning, testing, deployment, and rollback management
    17 repo stars
81. ▌
    Nextjs Performance Tuning · gabrielmoreira

    Steps and audit checklists for Next.js rendering optimizations, layout shift prevention, and static bundle chunking.
    17 repo stars
82. ▌
    Typescript Strict Refactor · gabrielmoreira

    Refactor existing JavaScript or loosely-typed TypeScript code to strict TypeScript - eliminating 'any', adding explicit types, and using zod-derived types. Use when asked to "type this", "convert to TypeScript", "fix type errors", or "make this strict-mode compliant".
    17 repo stars
83. ▌
    Setting Up Compose Hotswan · gabrielmoreira

    Use this skill to install and verify Compose HotSwan end to end so a developer goes from zero to working sub-second hot reload on a real device or emulator in one session. Covers the JetBrains IDE plugin install, the `com.github.skydoves.compose.hotswan.compiler` Gradle plugin wiring, the canonical `hotSwanCompiler { enabled = true; debugOnly = true }` DSL block, the HotSwan tool window flow, and the first save-to-reload verification. Trigger when the user mentions HotSwan, Compose hot reload, instant UI update, "save and see", "no rebuild", live edit on device, fast Compose iteration, or already has the JetBrains plugin installed and asks how to apply the Gradle compiler plugin.
    17 repo stars
84. ▌
    Choosing Derivedstateof · gabrielmoreira

    Use this skill to decide when Jetpack Compose derivedStateOf is the right tool and when it is pure overhead. Covers the "input frequency must exceed output frequency" rule, the mandatory remember { derivedStateOf { } } wrapper, the canonical pitfall of capturing non-state variables by initial value (and the remember(key) fix), and the snapshotFlow alternative for fire-and-forget side effects on derived values. Use when the developer mentions derivedStateOf, scroll-position-driven booleans, threshold checks, firstVisibleItemIndex, "show FAB on scroll", recomposition counts that don't drop after wrapping a value, or asks whether a computed string concatenation should use derivedStateOf.
    17 repo stars
85. ▌
    Controlflow Executability Verifier · gabrielmoreira bundle

    Use when a saved plan should be tested for cold-start executability before coding, especially for large tasks, weak-confidence plans, or plans whose early phases may be too vague for a fresh executor to follow without hidden context.
    17 repo stars
86. ▌
    Offensive Dependency Confusion · gabrielmoreira

    Deep-dive offensive methodology for dependency confusion and namespace attacks across all major package ecosystems. Covers npm scope confusion exploiting the gap between public and private scoped packages and .npmrc misconfigurations where registry mappings fail to pin internal scopes exclusively. Addresses PyPI namespace attacks through --extra-index-url resolution ordering, NuGet feed priority exploitation when multiple package sources are configured without clear directives, Maven and Gradle repository ordering where artifact resolution traverses repositories sequentially, Go module proxy abuse through GOPROXY misconfiguration, Ruby gems namespace squatting, and Docker image tag confusion with unqualified image references. Provides complete proof-of-concept methodology using safe callbacks including DNS canary via interactsh or Burp Collaborator and HTTP beacon with no destructive payload. Covers reconnaissance techniques for discovering internal package names through GitHub repository analysis, error mess
    17 repo stars
87. ▌
    Binding Site Characterization · gabrielmoreira

    Binding Site Characterization - Characterize binding sites: predict pockets with fpocket and P2Rank, get binding site info from ChEMBL, and visualize. Use this skill for structural biology tasks involving run fpocket pred pocket prank get binding site by id visualize protein. Combines 4 tools from 3 SCP server(s).
    17 repo stars
88. ▌
    Chemical Structure Comparison · gabrielmoreira

    Chemical Structure Comparison - Compare chemical structures: get SMILES, analyze structures, compute similarity, and check PubChem records. Use this skill for cheminformatics tasks involving NameToSMILES ChemicalStructureAnalyzer calculate smiles similarity get compound by name. Combines 4 tools from 4 SCP server(s).
    17 repo stars
89. ▌
    Molecular Visualization Suite · gabrielmoreira

    Molecular Visualization Suite - Visualize molecules: convert SMILES to formats, visualize molecule, visualize protein, visualize complex. Use this skill for chemical visualization tasks involving convert smiles to format visualize molecule visualize protein visualize complex. Combines 4 tools from 1 SCP server(s).
    17 repo stars
90. ▌
    Optical Frequency Calculation · gabrielmoreira

    Calculate optical frequency and wavelength relationships for photonics and electromagnetic analysis.
    17 repo stars
91. ▌
    Seawater Freezing Temperature · gabrielmoreira

    Calculate the freezing point temperature of seawater from absolute salinity and pressure using GSW thermodynamic equations.
    17 repo stars
92. ▌
    Smiles Comprehensive Analysis · gabrielmoreira

    SMILES Comprehensive Analysis - Comprehensive SMILES analysis: validate, convert name, compute all molecular descriptors, and predict ADMET. Use this skill for cheminformatics tasks involving is valid smiles ChemicalStructureAnalyzer calculate mol basic info pred molecule admet. Combines 4 tools from 3 SCP server(s).
    17 repo stars
93. ▌
    Variant Clinical Significance · gabrielmoreira

    Query NCBI ClinVar for variant clinical pathogenicity classification (Pathogenic/Benign/VUS), review status and associated diseases.
    17 repo stars
94. ▌
    Variant Functional Prediction · gabrielmoreira

    Query FAVOR API for variant functional prediction scores (CADD, SIFT, PolyPhen, REVEL, etc.) and gene annotation.
    17 repo stars
95. ▌
    Agent Activity Logger · gabrielmoreira

    Background reference skill defining the structured JSON log format written to logs/copilot/agent-activity.log by each phase agent on completion. Auto-loaded by Discuss, Research, Planner, TDD Implementer, and Verify agents when they append their completion log entry. Defines all required fields (timestamp, issueId, phase, agent, developer, status, summary, decisions, outputFile, nextPhase) and optional phase-specific fields (filesChanged for execute, testResults for verify). Also provides jq query examples for filtering logs by Issue, date, or status. Loads when log format, activity log, or agent logging is mentioned.
    17 repo stars
96. ▌
    Syncfusion Maui AI Assistview · gabrielmoreira bundle

    Implements Syncfusion .NET MAUI AI AssistView (SfAIAssistView) for AI-powered interactive chat interfaces. Use when working with AI chat interfaces, AI AssistView, SfAIAssistView, conversational UI, or chat with AI responses. Covers integrating AI services, creating chat UIs, implementing conversation flows, managing AI requests/responses, and displaying AI suggestions.
    17 repo stars
97. ▌
    Syncfusion Maui Digital Gauge · gabrielmoreira bundle

    Implements Syncfusion .NET MAUI DigitalGauge (SfDigitalGauge) control to display alphanumeric characters in LED-style digital format. Use when working with digital gauges, LED displays, seven-segment displays, digital clocks, or digital counters. Ideal for displaying numbers, letters, or special characters in a digital/electronic display format.
    17 repo stars
98. ▌
    Syncfusion Maui Funnel Charts · gabrielmoreira bundle

    Implements and customize Syncfusion .NET MAUI Funnel Charts (SfFunnelChart). Use when implementing funnel charts, sales funnel visualization, conversion funnel analysis, process stage visualization, or marketing funnel tracking. Covers funnel chart implementation, customization, data labels, legends, tooltips, segment spacing, and orientation.
    17 repo stars
99. ▌
    Syncfusion Maui Numeric Entry · gabrielmoreira bundle

    Implements Syncfusion .NET MAUI Numeric Entry control. Use when working with numeric input with validation, formatting (currency, percentage, decimal), value increment/decrement buttons, or range restrictions. Ideal for price inputs, quantity selectors, percentage calculators, or numeric data entry with custom formats.
    17 repo stars
100. ▌
     Syncfusion Maui Parallax View · gabrielmoreira bundle

     Implements Syncfusion .NET MAUI Parallax View (SfParallaxView) to create parallax scrolling effects where background elements move slower than foreground content. Use when working with parallax effects, parallax scrolling, background scroll effects, or depth scrolling. Covers both simple image parallax and complex custom control implementations for ScrollView and ListView.
     17 repo stars