Use when configuring artifacts for inter-job data passing or caching for faster builds. Covers cache strategies and artifact management.
Extract, translate and save arXiv CS.CV papers for a specific date. Use when user asks to fetch arXiv papers, download paper lists, extract CV papers, translate paper titles to…
Use when summoning Rune agents, when encountering "agent not found" errors, when selecting which review agents to use, or when checking agent capabilities and tools.
Aspen Plus integration skill for steady-state process simulation, thermodynamic modeling, and equipment rating
Use when applying Atomic Design methodology to organize UI components into quarks, atoms, molecules, organisms, templates, and pages. Core principles and hierarchy.
Use when building complex organisms from molecules and atoms like headers, footers, product cards, and sidebars. Organisms are distinct UI sections.
Use when creating page layouts without real content. Templates define the skeletal structure of pages using organisms, molecules, and atoms.
Statistical and non-statistical audit sampling skill with sample size determination and evaluation
AutoDock molecular docking skill for small molecule binding prediction and virtual screening
Design consultation: understands your product, researches the landscape, proposes a complete design system (aesthetic, typography, color, layout, spacing, motion), and ge — from…
Generate alignment statistics using samtools flagstat, stats, depth, and coverage. Use when assessing alignment quality, calculating coverage, or generating QC reports.
Align CLIP-seq reads to the genome with crosslink site awareness. Use when mapping preprocessed CLIP reads for peak calling. — from bg-szy/TOP-SKILLS
Detect horizontal gene transfer events using HGTector, compositional analysis, and phylogenetic incongruence methods.
Analyze genome collinearity and syntenic blocks using MCScanX, SyRI, and JCVI for comparative genomics.
Create circular genome visualizations with Circos and pyCircos. Display multi-track data including ideograms, genes, variants, CNVs, and interaction arcs.
Generate genome browser visualizations using pyGenomeTracks or IGV batch scripting for publication figures.
Create genome browser-style visualizations showing multiple data tracks (coverage, peaks, genes) using pyGenomeTracks, Gviz, and IGV.
Designs experiments to minimize and account for batch effects using balanced layouts and blocking strategies.
Applies multiple testing correction methods including FDR, Bonferroni, and q-value for genomics data.
Calculates statistical power and minimum sample sizes for RNA-seq, ATAC-seq, and other sequencing experiments.
Estimates required sample sizes for differential expression, ChIP-seq, methylation, and proteomics studies.
Polish genome assemblies to reduce errors using short reads (Pilon), long reads (Racon), or ONT-specific tools (medaka).
Assess genome assembly quality using QUAST for contiguity metrics and BUSCO for completeness. Essential for evaluating assembly success and comparing assemblers.
Detect contamination and assess genome quality using CheckM, CheckM2, GTDB-Tk, and GUNC for metagenome-assembled genomes and isolate assemblies.
High-quality genome assembly from PacBio HiFi reads using hifiasm with phasing support. Use when building reference-quality diploid assemblies from HiFi data, especially with trio…
De novo genome assembly from Oxford Nanopore or PacBio long reads using Flye and Canu. Produces highly contiguous assemblies suitable for complete bacterial genomes and r — from…
Metagenome assembly from long reads using metaFlye and metaSPAdes with binning strategies. Use when reconstructing genomes from microbial communities, recovering…
Scaffold contigs into chromosome-level assemblies using Hi-C data with YaHS, 3D-DNA, SALSA2, and validate with BUSCO and contact maps.
De novo genome assembly from Illumina short reads using SPAdes. Covers bacterial, fungal, and small eukaryotic genome assembly, as well as metagenome and transcriptome assembly…
BED file format fundamentals, creation, validation, and basic operations. Covers BED3 through BED12 formats, coordinate systems, sorting, and format conversion using bedtools and…
Create and read bigWig browser tracks for visualizing continuous genomic data. Convert bedGraph to bigWig, extract signal values, and generate coverage tracks using UCSC — from…
Calculate read depth and coverage across genomic intervals using bedtools genomecov and coverage. Generate bedGraph files, compute per-base depth, and summarize coverage…
Parse, query, and convert GTF and GFF3 annotation files. Extract gene, transcript, and exon coordinates using gffread, gtfparse, and gffutils.
Core interval arithmetic operations including intersect, subtract, merge, complement, map, and groupby using bedtools and pybedtools.
Find nearest features, search within windows, and extend intervals using closest, window, flank, and slop operations.
Download, prepare, and manage reference panels for phasing and imputation. Covers 1000 Genomes, HRC, and TOPMed panels.
Calculate linkage disequilibrium statistics (r², D'), perform LD pruning for population structure analysis, identify haplotype blocks, and visualize LD patterns using PLI — from…
Python population genetics with scikit-allel. Read VCF files, compute allele frequencies, calculate diversity statistics, perform PCA, and run selection scans using Genot — from…
Detect signatures of natural selection using Fst, Tajima's D, iHS, XP-EHH, and other selection statistics.
Validate PCR primers for specificity, dimers, hairpins, and secondary structures using primer3-py thermodynamic calculations.
Design qPCR primers and TaqMan/molecular beacon probes using primer3-py. Configure probe Tm, primer-probe spacing, and hydrolysis probe constraints for real-time PCR assa — from…
Align DNA short reads to reference genomes using bwa-mem2, the faster successor to BWA-MEM. Use when aligning DNA short reads to a reference genome. — from bg-szy/TOP-SKILLS
Creates reproducible Jupyter notebooks for bioinformatics analysis with parameterization using papermill.
Create reproducible bioinformatics analysis reports with R Markdown including code, results, and visualizations in HTML, PDF, or Word format.
Multi-omic biomarker discovery studio that ingests expression + metadata, performs QC, multi-strategy feature selection, nested CV model training, survival analysis hooks, and…
Calculate sequence properties like GC content, molecular weight, isoelectric point, and GC skew using Biopython.
Build tissue and condition-specific metabolic models using GIMME, iMAT, and INIT algorithms with expression data constraints.
Perform flux balance analysis (FBA) and flux variability analysis (FVA) on genome-scale metabolic models using COBRApy.
Perform in silico gene knockout analysis and synthetic lethality screens using COBRApy single and double deletions.
Build genome-scale metabolic models from genome sequences using CarveMe and gapseq for automated reconstruction. Generate draft models ready for curation and analysis.
Validate, gap-fill, and curate genome-scale metabolic models using memote for quality scores and COBRApy for manual curation.
Clinical variant interpretation using ClinVar, ACMG guidelines, and pathogenicity predictors. Prioritize variants for diagnostic and research applications.
Generate variant statistics, sample concordance, and quality metrics using bcftools stats and gtcheck.
Create portable, standards-based bioinformatics pipelines with Common Workflow Language (CWL). Use when building workflows that need maximum portability across execution — from…
Create scalable, containerized bioinformatics pipelines with Nextflow DSL2 supporting Docker, Singularity, and cloud execution.
Build reproducible bioinformatics pipelines with Snakemake using rules, wildcards, and automatic dependency resolution.
Create portable bioinformatics pipelines with Workflow Description Language (WDL) using Cromwell or miniwdl execution engines.
End-to-end CRISPR experiment design from target selection to delivery-ready constructs. Covers guide RNA design, off-target assessment, and specialized editing strategies…
End-to-end CRISPR screen analysis from FASTQ to hit genes. Orchestrates guide counting, QC, statistical analysis with MAGeCK, and hit calling with multiple methods.
End-to-end flow cytometry workflow from FCS files to differential analysis. Orchestrates compensation, transformation, gating/clustering, and statistical testing with CAT — from…