Expert skill for AMBA AXI protocol implementation and verification in FPGA designs
GLAW back-tax & IRS-collections seat — resolve a delinquent taxpayer end-to-end: file the missing years (built from the general ledger), replace any IRS Substitute-for-Return,…
Pedantic Diversio backend dev workflow Skill that enforces ClickUp-linked branch/PR naming, PR hygiene, safe Django migrations, and downtime-safe schema changes for…
Create a structured plan directory with Ralph Wiggum Loop integration for backend Django projects. Generates PLAN.md (task index), task files, and RALPH-PROMPT.md (the actual…
Integrates with background check services, social media analysis, reference verification
Search BAILII for UK case law and retrieve full judgment text. Use when someone asks to find a case, search for case law on a topic, read a judgment, or check how courts have…
Analysis skill for detecting and mitigating barren plateaus in variational circuits
Base L2 automation toolkit for AI agents. Includes Litcoiin mining automation, Bankr wallet operations, ClawBank treasury management, and Base-native DeFi interactions.
Use when multiple fix attempts fail and you need to systematically restore to a working baseline and reimplement instead of fixing broken code.
Bayesian probabilistic reasoning for prior specification, posterior computation, and belief updating
Bayesian network construction and inference skill for probabilistic reasoning, causal analysis, and belief updating
Detect and fix content overflow, cutoff, and clipping issues in Beamer LaTeX slide decks. Renders each PDF page as an image, visually inspects for clipped TikZ diagrams, text…
Soil bearing capacity calculation skill using multiple methods for various foundation types
Use when a long session has compacted or handed off, before any Edit, to confirm Claude's belief about file contents still matches disk.
Benchmarking study skill for internal, competitive, and best-in-class performance comparison
Manage benefits enrollment and administration workflows including elections, life events, open enrollment, and compliance tracking
BIM clash detection skill for identifying and managing coordination conflicts between disciplines
Filter alignments by flags, mapping quality, and regions using samtools view and pysam. Use when extracting specific reads, removing low-quality alignments, or subsetting — from…
Create and use BAI/CSI indices for BAM/CRAM files using samtools and pysam. Use when enabling random access to alignment files or fetching specific genomic regions.
Sort alignment files by coordinate or read name using samtools and pysam. Use when preparing BAM files for indexing, variant calling, or paired-end analysis.
Validate alignment quality with insert size distribution, proper pairing rates, GC bias, strand balance, and other post-alignment metrics.
Identify enriched sequence motifs at CLIP-seq binding sites for RBP binding specificity. Use when characterizing the sequence preferences of an RNA-binding protein.
Call protein-RNA binding site peaks from CLIP-seq data using CLIPper, PureCLIP, or Piranha. Use when identifying RBP binding sites from aligned CLIP reads. — from bg-szy/TOP-SKILLS
Preprocess CLIP-seq data including adapter trimming, UMI extraction, and PCR duplicate removal. Use when preparing raw CLIP, iCLIP, or eCLIP reads for peak calling.
Reconstruct ancestral sequences at phylogenetic nodes using PAML and IQ-TREE marginal likelihood methods.
Infer orthologous gene groups across species using OrthoFinder and ProteinOrtho. Identify orthologs, paralogs, and co-orthologs for comparative genomics and functional annotation…
Generate consensus FASTA sequences by applying VCF variants to a reference using bcftools consensus. Use when creating sample-specific reference sequences or reconstructi — from…
Select and apply colorblind-friendly palettes for scientific figures using viridis, RColorBrewer, and custom color schemes.
Create publication-quality scientific figures with ggplot2 including scatter plots, boxplots, heatmaps, and multi-panel layouts.
Create clustered heatmaps with row/column annotations using ComplexHeatmap, pheatmap, and seaborn for gene expression and omics data visualization.
Create interactive HTML plots with plotly and bokeh for exploratory data analysis and web-based sharing of omics visualizations.
Combine multiple plots into publication-ready multi-panel figures using patchwork, cowplot, or matplotlib GridSpec with shared legends and panel labels.
Reusable plotting functions for common omics visualizations. Custom ggplot2/matplotlib implementations of volcano, MA, PCA, enrichment dotplots, boxplots, and survival cu — from…
Create UpSet plots to visualize set intersections as an alternative to Venn diagrams using UpSetR or upsetplot.
Create publication-ready volcano plots with custom thresholds, gene labels, and highlighting using ggplot2, EnhancedVolcano, or matplotlib.
Mark and remove PCR/optical duplicates using samtools fixmate and markdup. Use when preparing alignments for variant calling or when duplicate reads would bias analysis.
Load gene expression count matrices from various formats including CSV, TSV, featureCounts, Salmon, kallisto, and 10X.
Convert between gene identifier systems including Ensembl, Entrez, HGNC symbols, and UniProt. Use when mapping IDs for pathway analysis or matching different data sources — from…
Merge sample metadata with count matrices and add gene annotations. Use when preparing data for differential expression analysis or visualization.
Work with sparse matrices for memory-efficient storage of count data. Use when dealing with single-cell data or large bulk RNA-seq datasets where most values are zero.
Variant calling with GATK HaplotypeCaller following best practices. Covers germline SNP/indel calling, GVCF workflow for cohorts, joint genotyping, and variant quality sc — from…
Cell-free DNA analysis pipeline from plasma sequencing to tumor monitoring. Preprocesses cfDNA reads, analyzes fragment patterns, estimates tumor fraction from sWGS, and — from…
Run local BLAST searches using BLAST+ command-line tools. Use when running fast unlimited searches, building custom databases, performing large-scale analysis, or when NC — from…
Maps query single-cell data to reference atlases using scArches transfer learning with scVI and scANVI models.
Selects informative features for biomarker discovery using Boruta all-relevant selection, mRMR minimum redundancy, and LASSO regularization.
Implements nested cross-validation and stratified splits for unbiased model evaluation on biomedical datasets.
Builds classification models for omics data using RandomForest, XGBoost, and logistic regression with sklearn-compatible APIs.
Explains machine learning predictions on omics data using SHAP values and LIME for feature attribution. Identifies which genes or features drive classifier decisions.
Analyzes time-to-event data using Kaplan-Meier curves, log-rank tests, and Cox proportional hazards regression with lifelines.
Impute missing genotypes using reference panels with Beagle or Minimac4. Use when increasing variant density for GWAS, harmonizing data across genotyping platforms, or in — from…
Phase genotypes into haplotypes using Beagle or SHAPEIT. Resolves which alleles are inherited together on each chromosome.
Quality control of phasing and imputation results. Filter by INFO scores, assess accuracy, and prepare imputed data for downstream analysis.
Build maximum likelihood phylogenetic trees using IQ-TREE2 and RAxML-ng. Use when inferring publication-quality trees with model selection, ultrafast bootstrap, or partitioned…
Generate pileup data for variant calling using samtools mpileup and pysam. Use when preparing data for variant calling, analyzing per-position read data, or calculating a — from…
PLINK file formats, format conversion, and quality control filtering for population genetics. Convert between VCF, BED/BIM/FAM, and PED/MAP formats, apply MAF, genotyping — from…
Analyze population structure using PCA and admixture analysis with PLINK and ADMIXTURE. Identify population clusters, assess ancestry proportions, visualize genetic struc — from…
Design PCR primers for a target sequence using primer3-py. Specify target regions, product size, melting temperature, and other constraints.
Align short reads using Bowtie2 with local or end-to-end modes. Supports gapped alignment. Use when aligning ChIP-seq, ATAC-seq, or when flexible alignment modes are need — from…
Align RNA-seq reads with HISAT2, a memory-efficient splice-aware aligner. Use when STAR's memory requirements are too high or for general RNA-seq alignment.
Generate consensus sequences and manage reference files using samtools. Use when creating consensus from alignments, indexing references, or creating sequence dictionarie — from…