Operacions amb fitxers
Manipulació i gestió de fitxers
bio-alignment-indexing
GPTomics
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.
bio-chipseq-qc
GPTomics
ChIP-seq quality control metrics including FRiP (Fraction of Reads in Peaks), cross-correlation analysis (NSC/RSC), library complexity, and IDR (Irreproducibility Discovery Rate) for replicate concordance. Use to assess experiment quality before downstream analysis. Use when assessing ChIP-seq data quality metrics.
bio-differential-splicing
GPTomics
Detects differential alternative splicing between conditions using rMATS-turbo (BAM-based) or SUPPA2 diffSplice (TPM-based). Reports events with FDR-corrected significance and delta PSI effect sizes. Use when comparing splicing patterns between treatment groups, tissues, or disease states.
bio-alignment-msa-parsing
GPTomics
Parse and analyze multiple sequence alignments using Biopython. Extract sequences, identify conserved regions, analyze gaps, work with annotations, and manipulate alignment data for downstream analysis. Use when parsing or manipulating multiple sequence alignments.
bio-molecular-io
GPTomics
Reads, writes, and converts molecular file formats (SMILES, SDF, MOL2, PDB) using RDKit and Open Babel. Handles structure parsing, canonicalization, and full standardization pipeline including sanitization, normalization, and tautomer canonicalization. Use when loading chemical libraries, converting formats, or preparing molecules for analysis.
bio-reference-operations
GPTomics
Generate consensus sequences and manage reference files using samtools. Use when creating consensus from alignments, indexing references, or creating sequence dictionaries.
bio-chipseq-motif-analysis
GPTomics
De novo motif discovery and known motif enrichment analysis using HOMER and MEME-ChIP. Identify transcription factor binding motifs in ChIP-seq, ATAC-seq, or other genomic peak data. Use when finding enriched DNA motifs in peak sequences.
packages-documentation
reactive
Write, update, and format docs for public APIs - API reference, README, docstrings, usage examples, migration guides, deprecation notices
bio-sam-bam-basics
GPTomics
View, convert, and understand SAM/BAM/CRAM alignment files using samtools and pysam. Use when inspecting alignments, converting between formats, or understanding alignment file structure.
bio-alignment-filtering
GPTomics
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.
bio-alignment-io
GPTomics
Read, write, and convert multiple sequence alignment files using Biopython Bio.AlignIO. Supports Clustal, PHYLIP, Stockholm, FASTA, Nexus, and other alignment formats for phylogenetics and conservation analysis. Use when reading, writing, or converting alignment file formats.
bio-atac-seq-atac-peak-calling
GPTomics
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.
bio-virtual-screening
GPTomics
Performs structure-based virtual screening using AutoDock Vina 1.2 for molecular docking. Prepares receptor PDBQT files, generates ligand conformers, defines binding site boxes, and ranks compounds by predicted binding affinity. Use when screening chemical libraries against a protein structure to find potential binders.
bio-substructure-search
GPTomics
Searches molecular libraries for substructure matches using SMARTS patterns with RDKit. Filters compounds by pharmacophore features, functional groups, or scaffold matches with atom mapping. Use when finding compounds containing specific chemical moieties or filtering libraries by structural features.
bio-causal-genomics-fine-mapping
GPTomics
Identify likely causal variants within GWAS loci using SuSiE for sum of single effects regression and FINEMAP for shotgun stochastic search. Computes posterior inclusion probabilities and credible sets to prioritize variants for functional follow-up. Use when narrowing GWAS association signals to candidate causal variants or building credible sets for functional validation.
dashboard-create-screen
Automattic
Create a new screen in the Multi-site Dashboard with automatic route registration
too-long-skill
pproenca
This skill has more than 500 lines which should fail validation.
aws-sdk-java-v2-s3
giuseppe-trisciuoglio
Provides Amazon S3 patterns and examples using AWS SDK for Java 2.x. Use when working with S3 buckets, uploading/downloading objects, multipart uploads, presigned URLs, S3 Transfer Manager, object operations, or S3-specific configurations.
chunking-strategy
giuseppe-trisciuoglio
Provides optimal chunking strategies in RAG systems and document processing pipelines. Use when building retrieval-augmented generation systems, vector databases, or processing large documents that require breaking into semantically meaningful segments for embeddings and search.
missing-references
pproenca
This skill references rules that do not have corresponding files in the references directory.
elixir-essentials
j-morgan6
MANDATORY for ALL Elixir code changes. Invoke before writing any .ex or .exs file.
stacks-marketing-directory-submissions
stacksjs
Use when the user wants to submit their product to startup, SaaS, AI, agent, MCP, no-code, or review directories for backlinks, domain rating, and discovery. Covers marketing planning and its Stacks implementation.
stacks-logging
stacksjs
Use when implementing logging in Stacks - the log facade (info, error, warn, debug, success), dump/dd debugging, timing functions, file-based logging, or log configuration. Covers @stacksjs/logging and config/logging.ts.
stacks-marketing-copy-editing
stacksjs
Use when the user wants to edit, review, or improve existing marketing copy, or refresh outdated content. Covers marketing planning and its Stacks implementation.