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Call accessible chromatin regions from ATAC-seq data using MACS3 with ATAC-specific parameters. Use when identifying open chromatin regions from aligned ATAC-seq BAM files, different from ChIP-seq peak calling.
Gene Ontology over-representation analysis using clusterProfiler enrichGO. Tests whether GO terms are enriched in a gene list compared to background. Supports all three ontologies (BP, MF, CC), multiple ID type...
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...
End-to-end DNA sequencing workflow from FASTQ files to variant calls. Covers QC, alignment with BWA, BAM processing, and variant calling with bcftools or GATK HaplotypeCaller.
Calculate sequence statistics (N50, length distribution, GC content, summary reports) using Biopython. Use when analyzing sequence datasets, generating QC reports, or comparing assemblies.
Comprehensive variant annotation using bcftools annotate/csq, VEP, SnpEff, and ANNOVAR. Add database annotations, predict functional consequences, and assess clinical significance.
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 or Hi-C phasing for fully reso...
Workflow from differential expression results to functional enrichment analysis. Covers GO, KEGG, Reactome enrichment with clusterProfiler and visualization.
Access UniProt protein database for sequences, annotations, and functional information. Use when you need protein data, GO terms, domain annotations, or protein-protein interactions.
Annotate CNVs with genes, pathways, and clinical significance. Use to interpret CNV calls and identify affected genes.
Build, manage, and search spectral libraries for proteomics. Covers DDA-based library generation, predicted libraries (Prosit, DeepLC), and library formats.
Analyze restriction digest fragments using Biopython Bio.Restriction. Predict fragment sizes, get fragment sequences, simulate gel electrophoresis patterns, and perform double digests.
Track bacterial strains using MASH, sourmash, fastANI, and inStrain. Compare genomes, detect contamination, and monitor strain-level variation. Use when needing sub-species resolution for outbreak tracking, tra...
Differential binding analysis using DiffBind. Compare ChIP-seq peaks between conditions with statistical rigor. Requires replicate samples. Outputs differentially bound regions with fold changes and p-values.
End-to-end proteomics workflow from MaxQuant output to differential protein abundance. Orchestrates data import, normalization, imputation, and statistical testing with MSstats or limma.
Navigate protein structure hierarchy using Biopython Bio.PDB SMCRA model. Use for accessing models, chains, residues, and atoms, iterating over structure levels, extracting sequences, identifying residue types,...
Create genome browser-style visualizations showing multiple data tracks (coverage, peaks, genes) using pyGenomeTracks, Gviz, and IGV. Use when visualizing genomic data at specific loci with multiple aligned tra...
Visualize ChIP-seq data using deepTools, Gviz, and ChIPseeker. Create heatmaps, profile plots, and genome browser tracks. Visualize signal around peaks, TSS, or custom regions.
Align RNA-seq reads with STAR (Spliced Transcripts Alignment to a Reference). Use for RNA-seq data requiring splice-aware alignment. Supports two-pass mode for novel splice junction discovery.
Guidelines for implementing audio feedback in web interfaces. Use when adding sound to interactions, reviewing audio UX, or designing notification systems. Triggers on tasks involving user feedback, confirmatio...
Best practices for implementing Android ViewModels, specifically focused on StateFlow for UI state and SharedFlow for one-off events.
Guidance on implementing the Data Layer using Repository pattern, Room (Local), and Retrofit (Remote) with offline-first synchronization.
Debug and optimize Android/Gradle build performance. Use when builds are slow, investigating CI/CD performance, analyzing build scans, or identifying compilation bottlenecks.
Authoritative rules and patterns for production-quality Kotlin Coroutines onto Android. Covers structured concurrency, lifecycle integration, and reactive streams.
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