712 skills found ¡ Page 23 of 24
spencermarx / V3 Deep IntegrationDeep agentic-flow@alpha integration implementing ADR-001. Eliminates 10,000+ duplicate lines by building claude-flow as specialized extension rather than parallel implementation.
spencermarx / github-code-reviewComprehensive GitHub code review with AI-powered swarm coordination
spencermarx / browserWeb browser automation with AI-optimized snapshots for claude-flow agents
jaechang-hits / statsmodels-statistical-modelingPython statistical modeling: regression (OLS, WLS, GLM), discrete (Logit, Poisson, NegBin), time series (ARIMA, SARIMAX, VAR), with rigorous inference, diagnostics, and hypothesis tests. Use scikit-learn for ML; statistical-analysis for test choice.
jaechang-hits / opencv-bioimage-analysisComputer vision for bio-image preprocessing, feature detection, real-time microscopy. Color conversion, morphology, contour/blob detection, template matching, optical flow on fluorescence/brightfield. 10-100Ã faster than pure Python via C++.
jaechang-hits / arboreto-grn-inferenceGRN inference from expression via GRNBoost2 (gradient boosting) or GENIE3 (Random Forest). Load matrix, filter by TFs, infer TF-target-importance links, save network. Dask-parallelized to single-cell scale. Core SCENIC component.
jaechang-hits / matlab-scientific-computingMATLAB/GNU Octave numerical computing: matrices, linear algebra, ODEs, signal processing, optimization, statistics, scientific visualization. MATLAB-syntax examples run on both. For Python use numpy/scipy; for statistical modeling use statsmodels.
jaechang-hits / nextflow-workflow-engineDataflow workflow engine for scalable bioinformatics pipelines. Defines processes (containerized tasks) connected by channels; runs local, HPC (SLURM/SGE), cloud (AWS/GCP/Azure), or Kubernetes via a single config change. Powers nf-core.
jaechang-hits / pymooPython framework for single- and multi-objective optimization with evolutionary algorithms. Define vectorized objectives and constraints; solve with NSGA-II, NSGA-III, MOEA/D, GAs, or differential evolution. Analyze Pareto fronts, visualize trade-offs, customize operators and callbacks.
jaechang-hits / pnas-figure-guidePNAS figure preparation: resolution (300-1000 PPI), formats (TIFF/EPS/PDF), strict RGB-only color, Arial/Helvetica fonts, italicized uppercase panel labels, automated image screening.
jaechang-hits / pytdc-therapeutics-data-commonsTherapeutics Data Commons (TDC) AI-ready drug discovery datasets. Curated ADME, toxicity, DTI, DDI with scaffold/cold splits, standardized metrics, molecular oracles, and ADMET benchmarks for therapeutic ML and property prediction.
jaechang-hits / samtools-bam-processingCLI toolkit for SAM/BAM/CRAM: sort, index, convert, filter, QC alignments. Core commands: view, sort, index, flagstat, stats, depth, markdup, merge. Required between alignment and variant/peak calling. Use pysam for Python-native BAM access; deeptools for normalized coverage tracks.
jaechang-hits / bakta-genome-annotationAnnotate bacterial and archaeal genomes and plasmids with Bakta's Prodigal/HMM/diamond pipeline. Identifies CDS, ncRNA, tRNA, rRNA, tmRNA, sORFs, CRISPR arrays, oriC/oriV/oriT, and gaps against a curated UniRef-derived database.
jaechang-hits / bedtools-genomic-intervalsGenomic interval ops on BED/BAM/GFF/VCF. Find overlaps, merge intervals, compute coverage, extract FASTA, find nearest features. Core for ChIP-seq peak annotation, region filtering, genome arithmetic. Use tabix for indexed single-region queries; use deeptools for normalized bigWig coverage.
jaechang-hits / deeptools-ngs-analysisNGS CLI for ChIP/RNA/ATAC-seq. BAMâbigWig with RPGC/CPM/RPKM, sample correlation/PCA, heatmaps/profiles around features, fingerprints. For alignment use STAR/BWA; for peak calling use MACS2.
jaechang-hits / pydeseq2-differential-expressionBulk RNA-seq DE with PyDESeq2: load counts, normalize, fit negative binomial models, Wald test (BH-FDR), LFC shrinkage, volcano/MA plots. Use for two-group comparisons, multi-factor designs with batch correction, multiple contrasts.
jaechang-hits / celltypist-cell-annotationAutomated scRNA-seq cell type annotation via pre-trained logistic regression. 45+ models: immune, gut, lung, brain, fetal, cancer microenvironments. Input normalized AnnData; outputs per-cell labels, majority-vote cluster labels, confidence scores.
jaechang-hits / cellxgene-censusQuery CELLxGENE Census (61M+ cells). Search by cell type/tissue/disease/organism; get AnnData, stream out-of-core, train PyTorch models. For your own data use scanpy; for annotated data use anndata.
giuseppe-trisciuoglio / memory-md-managementProvides comprehensive memory file management capabilities including auditing, quality assessment, and targeted improvements for files such as CLAUDE.md
giuseppe-trisciuoglio / unit-test-parameterizedProvides parameterized testing patterns with JUnit 5, generates data-driven unit tests using @ParameterizedTest, @ValueSource, @CsvSource, @MethodSource. Creates tests that run the same logic with multiple input values
giuseppe-trisciuoglio / unit-test-utility-methodsProvides patterns for testing utility classes, static methods, and helper functions. Validates pure functions, null handling, edge cases, and boundary conditions. Generates AssertJ assertions and @ParameterizedTest for string utils, math utils, validators, and collection helpers
giuseppe-trisciuoglio / notebooklmEnables interaction with Google NotebookLM for advanced RAG (Retrieval-Augmented Generation) capabilities via the notebooklm-mcp-cli tool
giuseppe-trisciuoglio / unit-test-bean-validationProvides patterns for unit testing Jakarta Bean Validation (JSR-380), including @Valid, @NotNull, @Min, @Max, @Email constraints with Hibernate Validator. Generates custom validator tests, constraint violation assertions, validation groups, and parameterized validation tests.
giuseppe-trisciuoglio / aws-cloudformation-cloudwatchProvides AWS CloudFormation patterns for CloudWatch monitoring, metrics, alarms, dashboards, logs, and observability
giuseppe-trisciuoglio / tailwind-design-systemSkill for creating and managing a Design System using Tailwind CSS and shadcn/ui
datadrivenconstruction / open-construction-estimateAccess and utilize open construction pricing databases. Match BIM elements to standardized work items, calculate costs using public unit price databases with 55,000+ work items.
datadrivenconstruction / resource-pool-optimizerOptimize shared resource pools across multiple construction projects. Balance resource allocation, minimize conflicts, and maximize utilization across the portfolio.
datadrivenconstruction / progress-photo-analyzerAnalyze construction site photos to track progress, detect safety issues, and compare against BIM models using computer vision.
datadrivenconstruction / ifc-to-excelConvert IFC files (2x3, 4x1, 4x3) to Excel databases using IfcExporter CLI. Extract BIM data, properties, and geometry without proprietary software.
AgriciDaniel / claude-repurposeContent Repurposing Engine for Claude Code. Turn 1 piece of content into 10+ platform-optimized posts for Twitter, LinkedIn, Instagram, Facebook, YouTube, Skool, Reddit, and newsletters.
