@saibolla/ada 0.1.2

package/skills/gget/SKILL.md

@@ -0,0 +1,869 @@
+---
+name: gget
+description: "Fast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST searches, AlphaFold structures, enrichment analysis. Best for interactive exploration, simple queries. For batch processing or advanced BLAST use biopython; for multi-database Python workflows use bioservices."
+license: BSD-2-Clause license
+metadata:
+    skill-author: K-Dense Inc.
+---
+
+# gget
+
+## Overview
+
+gget is a command-line bioinformatics tool and Python package providing unified access to 20+ genomic databases and analysis methods. Query gene information, sequence analysis, protein structures, expression data, and disease associations through a consistent interface. All gget modules work both as command-line tools and as Python functions.
+
+**Important**: The databases queried by gget are continuously updated, which sometimes changes their structure. gget modules are tested automatically on a biweekly basis and updated to match new database structures when necessary.
+
+## Installation
+
+Install gget in a clean virtual environment to avoid conflicts:
+
+```bash
+# Using uv (recommended)
+uv uv pip install gget
+
+# Or using pip
+uv pip install --upgrade gget
+
+# In Python/Jupyter
+import gget
+```
+
+## Quick Start
+
+Basic usage pattern for all modules:
+
+```bash
+# Command-line
+gget <module> [arguments] [options]
+
+# Python
+gget.module(arguments, options)
+```
+
+Most modules return:
+- **Command-line**: JSON (default) or CSV with `-csv` flag
+- **Python**: DataFrame or dictionary
+
+Common flags across modules:
+- `-o/--out`: Save results to file
+- `-q/--quiet`: Suppress progress information
+- `-csv`: Return CSV format (command-line only)
+
+## Module Categories
+
+### 1. Reference & Gene Information
+
+#### gget ref - Reference Genome Downloads
+
+Retrieve download links and metadata for Ensembl reference genomes.
+
+**Parameters**:
+- `species`: Genus_species format (e.g., 'homo_sapiens', 'mus_musculus'). Shortcuts: 'human', 'mouse'
+- `-w/--which`: Specify return types (gtf, cdna, dna, cds, cdrna, pep). Default: all
+- `-r/--release`: Ensembl release number (default: latest)
+- `-l/--list_species`: List available vertebrate species
+- `-liv/--list_iv_species`: List available invertebrate species
+- `-ftp`: Return only FTP links
+- `-d/--download`: Download files (requires curl)
+
+**Examples**:
+```bash
+# List available species
+gget ref --list_species
+
+# Get all reference files for human
+gget ref homo_sapiens
+
+# Download only GTF annotation for mouse
+gget ref -w gtf -d mouse
+```
+
+```python
+# Python
+gget.ref("homo_sapiens")
+gget.ref("mus_musculus", which="gtf", download=True)
+```
+
+#### gget search - Gene Search
+
+Locate genes by name or description across species.
+
+**Parameters**:
+- `searchwords`: One or more search terms (case-insensitive)
+- `-s/--species`: Target species (e.g., 'homo_sapiens', 'mouse')
+- `-r/--release`: Ensembl release number
+- `-t/--id_type`: Return 'gene' (default) or 'transcript'
+- `-ao/--andor`: 'or' (default) finds ANY searchword; 'and' requires ALL
+- `-l/--limit`: Maximum results to return
+
+**Returns**: ensembl_id, gene_name, ensembl_description, ext_ref_description, biotype, URL
+
+**Examples**:
+```bash
+# Search for GABA-related genes in human
+gget search -s human gaba gamma-aminobutyric
+
+# Find specific gene, require all terms
+gget search -s mouse -ao and pax7 transcription
+```
+
+```python
+# Python
+gget.search(["gaba", "gamma-aminobutyric"], species="homo_sapiens")
+```
+
+#### gget info - Gene/Transcript Information
+
+Retrieve comprehensive gene and transcript metadata from Ensembl, UniProt, and NCBI.
+
+**Parameters**:
+- `ens_ids`: One or more Ensembl IDs (also supports WormBase, Flybase IDs). Limit: ~1000 IDs
+- `-n/--ncbi`: Disable NCBI data retrieval
+- `-u/--uniprot`: Disable UniProt data retrieval
+- `-pdb`: Include PDB identifiers (increases runtime)
+
+**Returns**: UniProt ID, NCBI gene ID, primary gene name, synonyms, protein names, descriptions, biotype, canonical transcript
+
+**Examples**:
+```bash
+# Get info for multiple genes
+gget info ENSG00000034713 ENSG00000104853 ENSG00000170296
+
+# Include PDB IDs
+gget info ENSG00000034713 -pdb
+```
+
+```python
+# Python
+gget.info(["ENSG00000034713", "ENSG00000104853"], pdb=True)
+```
+
+#### gget seq - Sequence Retrieval
+
+Fetch nucleotide or amino acid sequences for genes and transcripts.
+
+**Parameters**:
+- `ens_ids`: One or more Ensembl identifiers
+- `-t/--translate`: Fetch amino acid sequences instead of nucleotide
+- `-iso/--isoforms`: Return all transcript variants (gene IDs only)
+
+**Returns**: FASTA format sequences
+
+**Examples**:
+```bash
+# Get nucleotide sequences
+gget seq ENSG00000034713 ENSG00000104853
+
+# Get all protein isoforms
+gget seq -t -iso ENSG00000034713
+```
+
+```python
+# Python
+gget.seq(["ENSG00000034713"], translate=True, isoforms=True)
+```
+
+### 2. Sequence Analysis & Alignment
+
+#### gget blast - BLAST Searches
+
+BLAST nucleotide or amino acid sequences against standard databases.
+
+**Parameters**:
+- `sequence`: Sequence string or path to FASTA/.txt file
+- `-p/--program`: blastn, blastp, blastx, tblastn, tblastx (auto-detected)
+- `-db/--database`:
+  - Nucleotide: nt, refseq_rna, pdbnt
+  - Protein: nr, swissprot, pdbaa, refseq_protein
+- `-l/--limit`: Max hits (default: 50)
+- `-e/--expect`: E-value cutoff (default: 10.0)
+- `-lcf/--low_comp_filt`: Enable low complexity filtering
+- `-mbo/--megablast_off`: Disable MegaBLAST (blastn only)
+
+**Examples**:
+```bash
+# BLAST protein sequence
+gget blast MKWMFKEDHSLEHRCVESAKIRAKYPDRVPVIVEKVSGSQIVDIDKRKYLVPSDITVAQFMWIIRKRIQLPSEKAIFLFVDKTVPQSR
+
+# BLAST from file with specific database
+gget blast sequence.fasta -db swissprot -l 10
+```
+
+```python
+# Python
+gget.blast("MKWMFK...", database="swissprot", limit=10)
+```
+
+#### gget blat - BLAT Searches
+
+Locate genomic positions of sequences using UCSC BLAT.
+
+**Parameters**:
+- `sequence`: Sequence string or path to FASTA/.txt file
+- `-st/--seqtype`: 'DNA', 'protein', 'translated%20RNA', 'translated%20DNA' (auto-detected)
+- `-a/--assembly`: Target assembly (default: 'human'/hg38; options: 'mouse'/mm39, 'zebrafinch'/taeGut2, etc.)
+
+**Returns**: genome, query size, alignment positions, matches, mismatches, alignment percentage
+
+**Examples**:
+```bash
+# Find genomic location in human
+gget blat ATCGATCGATCGATCG
+
+# Search in different assembly
+gget blat -a mm39 ATCGATCGATCGATCG
+```
+
+```python
+# Python
+gget.blat("ATCGATCGATCGATCG", assembly="mouse")
+```
+
+#### gget muscle - Multiple Sequence Alignment
+
+Align multiple nucleotide or amino acid sequences using Muscle5.
+
+**Parameters**:
+- `fasta`: Sequences or path to FASTA/.txt file
+- `-s5/--super5`: Use Super5 algorithm for faster processing (large datasets)
+
+**Returns**: Aligned sequences in ClustalW format or aligned FASTA (.afa)
+
+**Examples**:
+```bash
+# Align sequences from file
+gget muscle sequences.fasta -o aligned.afa
+
+# Use Super5 for large dataset
+gget muscle large_dataset.fasta -s5
+```
+
+```python
+# Python
+gget.muscle("sequences.fasta", save=True)
+```
+
+#### gget diamond - Local Sequence Alignment
+
+Perform fast local protein or translated DNA alignment using DIAMOND.
+
+**Parameters**:
+- Query: Sequences (string/list) or FASTA file path
+- `--reference`: Reference sequences (string/list) or FASTA file path (required)
+- `--sensitivity`: fast, mid-sensitive, sensitive, more-sensitive, very-sensitive (default), ultra-sensitive
+- `--threads`: CPU threads (default: 1)
+- `--diamond_db`: Save database for reuse
+- `--translated`: Enable nucleotide-to-amino acid alignment
+
+**Returns**: Identity percentage, sequence lengths, match positions, gap openings, E-values, bit scores
+
+**Examples**:
+```bash
+# Align against reference
+gget diamond GGETISAWESQME -ref reference.fasta --threads 4
+
+# Save database for reuse
+gget diamond query.fasta -ref ref.fasta --diamond_db my_db.dmnd
+```
+
+```python
+# Python
+gget.diamond("GGETISAWESQME", reference="reference.fasta", threads=4)
+```
+
+### 3. Structural & Protein Analysis
+
+#### gget pdb - Protein Structures
+
+Query RCSB Protein Data Bank for structure and metadata.
+
+**Parameters**:
+- `pdb_id`: PDB identifier (e.g., '7S7U')
+- `-r/--resource`: Data type (pdb, entry, pubmed, assembly, entity types)
+- `-i/--identifier`: Assembly, entity, or chain ID
+
+**Returns**: PDB format (structures) or JSON (metadata)
+
+**Examples**:
+```bash
+# Download PDB structure
+gget pdb 7S7U -o 7S7U.pdb
+
+# Get metadata
+gget pdb 7S7U -r entry
+```
+
+```python
+# Python
+gget.pdb("7S7U", save=True)
+```
+
+#### gget alphafold - Protein Structure Prediction
+
+Predict 3D protein structures using simplified AlphaFold2.
+
+**Setup Required**:
+```bash
+# Install OpenMM first
+uv pip install openmm
+
+# Then setup AlphaFold
+gget setup alphafold
+```
+
+**Parameters**:
+- `sequence`: Amino acid sequence (string), multiple sequences (list), or FASTA file. Multiple sequences trigger multimer modeling
+- `-mr/--multimer_recycles`: Recycling iterations (default: 3; recommend 20 for accuracy)
+- `-mfm/--multimer_for_monomer`: Apply multimer model to single proteins
+- `-r/--relax`: AMBER relaxation for top-ranked model
+- `plot`: Python-only; generate interactive 3D visualization (default: True)
+- `show_sidechains`: Python-only; include side chains (default: True)
+
+**Returns**: PDB structure file, JSON alignment error data, optional 3D visualization
+
+**Examples**:
+```bash
+# Predict single protein structure
+gget alphafold MKWMFKEDHSLEHRCVESAKIRAKYPDRVPVIVEKVSGSQIVDIDKRKYLVPSDITVAQFMWIIRKRIQLPSEKAIFLFVDKTVPQSR
+
+# Predict multimer with higher accuracy
+gget alphafold sequence1.fasta -mr 20 -r
+```
+
+```python
+# Python with visualization
+gget.alphafold("MKWMFK...", plot=True, show_sidechains=True)
+
+# Multimer prediction
+gget.alphafold(["sequence1", "sequence2"], multimer_recycles=20)
+```
+
+#### gget elm - Eukaryotic Linear Motifs
+
+Predict Eukaryotic Linear Motifs in protein sequences.
+
+**Setup Required**:
+```bash
+gget setup elm
+```
+
+**Parameters**:
+- `sequence`: Amino acid sequence or UniProt Acc
+- `-u/--uniprot`: Indicates sequence is UniProt Acc
+- `-e/--expand`: Include protein names, organisms, references
+- `-s/--sensitivity`: DIAMOND alignment sensitivity (default: "very-sensitive")
+- `-t/--threads`: Number of threads (default: 1)
+
+**Returns**: Two outputs:
+1. **ortholog_df**: Linear motifs from orthologous proteins
+2. **regex_df**: Motifs directly matched in input sequence
+
+**Examples**:
+```bash
+# Predict motifs from sequence
+gget elm LIAQSIGQASFV -o results
+
+# Use UniProt accession with expanded info
+gget elm --uniprot Q02410 -e
+```
+
+```python
+# Python
+ortholog_df, regex_df = gget.elm("LIAQSIGQASFV")
+```
+
+### 4. Expression & Disease Data
+
+#### gget archs4 - Gene Correlation & Tissue Expression
+
+Query ARCHS4 database for correlated genes or tissue expression data.
+
+**Parameters**:
+- `gene`: Gene symbol or Ensembl ID (with `--ensembl` flag)
+- `-w/--which`: 'correlation' (default, returns 100 most correlated genes) or 'tissue' (expression atlas)
+- `-s/--species`: 'human' (default) or 'mouse' (tissue data only)
+- `-e/--ensembl`: Input is Ensembl ID
+
+**Returns**:
+- **Correlation mode**: Gene symbols, Pearson correlation coefficients
+- **Tissue mode**: Tissue identifiers, min/Q1/median/Q3/max expression values
+
+**Examples**:
+```bash
+# Get correlated genes
+gget archs4 ACE2
+
+# Get tissue expression
+gget archs4 -w tissue ACE2
+```
+
+```python
+# Python
+gget.archs4("ACE2", which="tissue")
+```
+
+#### gget cellxgene - Single-Cell RNA-seq Data
+
+Query CZ CELLxGENE Discover Census for single-cell data.
+
+**Setup Required**:
+```bash
+gget setup cellxgene
+```
+
+**Parameters**:
+- `--gene` (-g): Gene names or Ensembl IDs (case-sensitive! 'PAX7' for human, 'Pax7' for mouse)
+- `--tissue`: Tissue type(s)
+- `--cell_type`: Specific cell type(s)
+- `--species` (-s): 'homo_sapiens' (default) or 'mus_musculus'
+- `--census_version` (-cv): Version ("stable", "latest", or dated)
+- `--ensembl` (-e): Use Ensembl IDs
+- `--meta_only` (-mo): Return metadata only
+- Additional filters: disease, development_stage, sex, assay, dataset_id, donor_id, ethnicity, suspension_type
+
+**Returns**: AnnData object with count matrices and metadata (or metadata-only dataframes)
+
+**Examples**:
+```bash
+# Get single-cell data for specific genes and cell types
+gget cellxgene --gene ACE2 ABCA1 --tissue lung --cell_type "mucus secreting cell" -o lung_data.h5ad
+
+# Metadata only
+gget cellxgene --gene PAX7 --tissue muscle --meta_only -o metadata.csv
+```
+
+```python
+# Python
+adata = gget.cellxgene(gene=["ACE2", "ABCA1"], tissue="lung", cell_type="mucus secreting cell")
+```
+
+#### gget enrichr - Enrichment Analysis
+
+Perform ontology enrichment analysis on gene lists using Enrichr.
+
+**Parameters**:
+- `genes`: Gene symbols or Ensembl IDs
+- `-db/--database`: Reference database (supports shortcuts: 'pathway', 'transcription', 'ontology', 'diseases_drugs', 'celltypes')
+- `-s/--species`: human (default), mouse, fly, yeast, worm, fish
+- `-bkg_l/--background_list`: Background genes for comparison
+- `-ko/--kegg_out`: Save KEGG pathway images with highlighted genes
+- `plot`: Python-only; generate graphical results
+
+**Database Shortcuts**:
+- 'pathway' → KEGG_2021_Human
+- 'transcription' → ChEA_2016
+- 'ontology' → GO_Biological_Process_2021
+- 'diseases_drugs' → GWAS_Catalog_2019
+- 'celltypes' → PanglaoDB_Augmented_2021
+
+**Examples**:
+```bash
+# Enrichment analysis for ontology
+gget enrichr -db ontology ACE2 AGT AGTR1
+
+# Save KEGG pathways
+gget enrichr -db pathway ACE2 AGT AGTR1 -ko ./kegg_images/
+```
+
+```python
+# Python with plot
+gget.enrichr(["ACE2", "AGT", "AGTR1"], database="ontology", plot=True)
+```
+
+#### gget bgee - Orthology & Expression
+
+Retrieve orthology and gene expression data from Bgee database.
+
+**Parameters**:
+- `ens_id`: Ensembl gene ID or NCBI gene ID (for non-Ensembl species). Multiple IDs supported when `type=expression`
+- `-t/--type`: 'orthologs' (default) or 'expression'
+
+**Returns**:
+- **Orthologs mode**: Matching genes across species with IDs, names, taxonomic info
+- **Expression mode**: Anatomical entities, confidence scores, expression status
+
+**Examples**:
+```bash
+# Get orthologs
+gget bgee ENSG00000169194
+
+# Get expression data
+gget bgee ENSG00000169194 -t expression
+
+# Multiple genes
+gget bgee ENSBTAG00000047356 ENSBTAG00000018317 -t expression
+```
+
+```python
+# Python
+gget.bgee("ENSG00000169194", type="orthologs")
+```
+
+#### gget opentargets - Disease & Drug Associations
+
+Retrieve disease and drug associations from OpenTargets.
+
+**Parameters**:
+- Ensembl gene ID (required)
+- `-r/--resource`: diseases (default), drugs, tractability, pharmacogenetics, expression, depmap, interactions
+- `-l/--limit`: Cap results count
+- Filter arguments (vary by resource):
+  - drugs: `--filter_disease`
+  - pharmacogenetics: `--filter_drug`
+  - expression/depmap: `--filter_tissue`, `--filter_anat_sys`, `--filter_organ`
+  - interactions: `--filter_protein_a`, `--filter_protein_b`, `--filter_gene_b`
+
+**Examples**:
+```bash
+# Get associated diseases
+gget opentargets ENSG00000169194 -r diseases -l 5
+
+# Get associated drugs
+gget opentargets ENSG00000169194 -r drugs -l 10
+
+# Get tissue expression
+gget opentargets ENSG00000169194 -r expression --filter_tissue brain
+```
+
+```python
+# Python
+gget.opentargets("ENSG00000169194", resource="diseases", limit=5)
+```
+
+#### gget cbio - cBioPortal Cancer Genomics
+
+Plot cancer genomics heatmaps using cBioPortal data.
+
+**Two subcommands**:
+
+**search** - Find study IDs:
+```bash
+gget cbio search breast lung
+```
+
+**plot** - Generate heatmaps:
+
+**Parameters**:
+- `-s/--study_ids`: Space-separated cBioPortal study IDs (required)
+- `-g/--genes`: Space-separated gene names or Ensembl IDs (required)
+- `-st/--stratification`: Column to organize data (tissue, cancer_type, cancer_type_detailed, study_id, sample)
+- `-vt/--variation_type`: Data type (mutation_occurrences, cna_nonbinary, sv_occurrences, cna_occurrences, Consequence)
+- `-f/--filter`: Filter by column value (e.g., 'study_id:msk_impact_2017')
+- `-dd/--data_dir`: Cache directory (default: ./gget_cbio_cache)
+- `-fd/--figure_dir`: Output directory (default: ./gget_cbio_figures)
+- `-dpi`: Resolution (default: 100)
+- `-sh/--show`: Display plot in window
+- `-nc/--no_confirm`: Skip download confirmations
+
+**Examples**:
+```bash
+# Search for studies
+gget cbio search esophag ovary
+
+# Create heatmap
+gget cbio plot -s msk_impact_2017 -g AKT1 ALK BRAF -st tissue -vt mutation_occurrences
+```
+
+```python
+# Python
+gget.cbio_search(["esophag", "ovary"])
+gget.cbio_plot(["msk_impact_2017"], ["AKT1", "ALK"], stratification="tissue")
+```
+
+#### gget cosmic - COSMIC Database
+
+Search COSMIC (Catalogue Of Somatic Mutations In Cancer) database.
+
+**Important**: License fees apply for commercial use. Requires COSMIC account credentials.
+
+**Parameters**:
+- `searchterm`: Gene name, Ensembl ID, mutation notation, or sample ID
+- `-ctp/--cosmic_tsv_path`: Path to downloaded COSMIC TSV file (required for querying)
+- `-l/--limit`: Maximum results (default: 100)
+
+**Database download flags**:
+- `-d/--download_cosmic`: Activate download mode
+- `-gm/--gget_mutate`: Create version for gget mutate
+- `-cp/--cosmic_project`: Database type (cancer, census, cell_line, resistance, genome_screen, targeted_screen)
+- `-cv/--cosmic_version`: COSMIC version
+- `-gv/--grch_version`: Human reference genome (37 or 38)
+- `--email`, `--password`: COSMIC credentials
+
+**Examples**:
+```bash
+# First download database
+gget cosmic -d --email user@example.com --password xxx -cp cancer
+
+# Then query
+gget cosmic EGFR -ctp cosmic_data.tsv -l 10
+```
+
+```python
+# Python
+gget.cosmic("EGFR", cosmic_tsv_path="cosmic_data.tsv", limit=10)
+```
+
+### 5. Additional Tools
+
+#### gget mutate - Generate Mutated Sequences
+
+Generate mutated nucleotide sequences from mutation annotations.
+
+**Parameters**:
+- `sequences`: FASTA file path or direct sequence input (string/list)
+- `-m/--mutations`: CSV/TSV file or DataFrame with mutation data (required)
+- `-mc/--mut_column`: Mutation column name (default: 'mutation')
+- `-sic/--seq_id_column`: Sequence ID column (default: 'seq_ID')
+- `-mic/--mut_id_column`: Mutation ID column
+- `-k/--k`: Length of flanking sequences (default: 30 nucleotides)
+
+**Returns**: Mutated sequences in FASTA format
+
+**Examples**:
+```bash
+# Single mutation
+gget mutate ATCGCTAAGCT -m "c.4G>T"
+
+# Multiple sequences with mutations from file
+gget mutate sequences.fasta -m mutations.csv -o mutated.fasta
+```
+
+```python
+# Python
+import pandas as pd
+mutations_df = pd.DataFrame({"seq_ID": ["seq1"], "mutation": ["c.4G>T"]})
+gget.mutate(["ATCGCTAAGCT"], mutations=mutations_df)
+```
+
+#### gget gpt - OpenAI Text Generation
+
+Generate natural language text using OpenAI's API.
+
+**Setup Required**:
+```bash
+gget setup gpt
+```
+
+**Important**: Free tier limited to 3 months after account creation. Set monthly billing limits.
+
+**Parameters**:
+- `prompt`: Text input for generation (required)
+- `api_key`: OpenAI authentication (required)
+- Model configuration: temperature, top_p, max_tokens, frequency_penalty, presence_penalty
+- Default model: gpt-3.5-turbo (configurable)
+
+**Examples**:
+```bash
+gget gpt "Explain CRISPR" --api_key your_key_here
+```
+
+```python
+# Python
+gget.gpt("Explain CRISPR", api_key="your_key_here")
+```
+
+#### gget setup - Install Dependencies
+
+Install/download third-party dependencies for specific modules.
+
+**Parameters**:
+- `module`: Module name requiring dependency installation
+- `-o/--out`: Output folder path (elm module only)
+
+**Modules requiring setup**:
+- `alphafold` - Downloads ~4GB of model parameters
+- `cellxgene` - Installs cellxgene-census (may not support latest Python)
+- `elm` - Downloads local ELM database
+- `gpt` - Configures OpenAI integration
+
+**Examples**:
+```bash
+# Setup AlphaFold
+gget setup alphafold
+
+# Setup ELM with custom directory
+gget setup elm -o /path/to/elm_data
+```
+
+```python
+# Python
+gget.setup("alphafold")
+```
+
+## Common Workflows
+
+### Workflow 1: Gene Discovery to Sequence Analysis
+
+Find and analyze genes of interest:
+
+```python
+# 1. Search for genes
+results = gget.search(["GABA", "receptor"], species="homo_sapiens")
+
+# 2. Get detailed information
+gene_ids = results["ensembl_id"].tolist()
+info = gget.info(gene_ids[:5])
+
+# 3. Retrieve sequences
+sequences = gget.seq(gene_ids[:5], translate=True)
+```
+
+### Workflow 2: Sequence Alignment and Structure
+
+Align sequences and predict structures:
+
+```python
+# 1. Align multiple sequences
+alignment = gget.muscle("sequences.fasta")
+
+# 2. Find similar sequences
+blast_results = gget.blast(my_sequence, database="swissprot", limit=10)
+
+# 3. Predict structure
+structure = gget.alphafold(my_sequence, plot=True)
+
+# 4. Find linear motifs
+ortholog_df, regex_df = gget.elm(my_sequence)
+```
+
+### Workflow 3: Gene Expression and Enrichment
+
+Analyze expression patterns and functional enrichment:
+
+```python
+# 1. Get tissue expression
+tissue_expr = gget.archs4("ACE2", which="tissue")
+
+# 2. Find correlated genes
+correlated = gget.archs4("ACE2", which="correlation")
+
+# 3. Get single-cell data
+adata = gget.cellxgene(gene=["ACE2"], tissue="lung", cell_type="epithelial cell")
+
+# 4. Perform enrichment analysis
+gene_list = correlated["gene_symbol"].tolist()[:50]
+enrichment = gget.enrichr(gene_list, database="ontology", plot=True)
+```
+
+### Workflow 4: Disease and Drug Analysis
+
+Investigate disease associations and therapeutic targets:
+
+```python
+# 1. Search for genes
+genes = gget.search(["breast cancer"], species="homo_sapiens")
+
+# 2. Get disease associations
+diseases = gget.opentargets("ENSG00000169194", resource="diseases")
+
+# 3. Get drug associations
+drugs = gget.opentargets("ENSG00000169194", resource="drugs")
+
+# 4. Query cancer genomics data
+study_ids = gget.cbio_search(["breast"])
+gget.cbio_plot(study_ids[:2], ["BRCA1", "BRCA2"], stratification="cancer_type")
+
+# 5. Search COSMIC for mutations
+cosmic_results = gget.cosmic("BRCA1", cosmic_tsv_path="cosmic.tsv")
+```
+
+### Workflow 5: Comparative Genomics
+
+Compare proteins across species:
+
+```python
+# 1. Get orthologs
+orthologs = gget.bgee("ENSG00000169194", type="orthologs")
+
+# 2. Get sequences for comparison
+human_seq = gget.seq("ENSG00000169194", translate=True)
+mouse_seq = gget.seq("ENSMUSG00000026091", translate=True)
+
+# 3. Align sequences
+alignment = gget.muscle([human_seq, mouse_seq])
+
+# 4. Compare structures
+human_structure = gget.pdb("7S7U")
+mouse_structure = gget.alphafold(mouse_seq)
+```
+
+### Workflow 6: Building Reference Indices
+
+Prepare reference data for downstream analysis (e.g., kallisto|bustools):
+
+```bash
+# 1. List available species
+gget ref --list_species
+
+# 2. Download reference files
+gget ref -w gtf -w cdna -d homo_sapiens
+
+# 3. Build kallisto index
+kallisto index -i transcriptome.idx transcriptome.fasta
+
+# 4. Download genome for alignment
+gget ref -w dna -d homo_sapiens
+```
+
+## Best Practices
+
+### Data Retrieval
+- Use `--limit` to control result sizes for large queries
+- Save results with `-o/--out` for reproducibility
+- Check database versions/releases for consistency across analyses
+- Use `--quiet` in production scripts to reduce output
+
+### Sequence Analysis
+- For BLAST/BLAT, start with default parameters, then adjust sensitivity
+- Use `gget diamond` with `--threads` for faster local alignment
+- Save DIAMOND databases with `--diamond_db` for repeated queries
+- For multiple sequence alignment, use `-s5/--super5` for large datasets
+
+### Expression and Disease Data
+- Gene symbols are case-sensitive in cellxgene (e.g., 'PAX7' vs 'Pax7')
+- Run `gget setup` before first use of alphafold, cellxgene, elm, gpt
+- For enrichment analysis, use database shortcuts for convenience
+- Cache cBioPortal data with `-dd` to avoid repeated downloads
+
+### Structure Prediction
+- AlphaFold multimer predictions: use `-mr 20` for higher accuracy
+- Use `-r` flag for AMBER relaxation of final structures
+- Visualize results in Python with `plot=True`
+- Check PDB database first before running AlphaFold predictions
+
+### Error Handling
+- Database structures change; update gget regularly: `uv pip install --upgrade gget`
+- Process max ~1000 Ensembl IDs at once with gget info
+- For large-scale analyses, implement rate limiting for API queries
+- Use virtual environments to avoid dependency conflicts
+
+## Output Formats
+
+### Command-line
+- Default: JSON
+- CSV: Add `-csv` flag
+- FASTA: gget seq, gget mutate
+- PDB: gget pdb, gget alphafold
+- PNG: gget cbio plot
+
+### Python
+- Default: DataFrame or dictionary
+- JSON: Add `json=True` parameter
+- Save to file: Add `save=True` or specify `out="filename"`
+- AnnData: gget cellxgene
+
+## Resources
+
+This skill includes reference documentation for detailed module information:
+
+### references/
+- `module_reference.md` - Comprehensive parameter reference for all modules
+- `database_info.md` - Information about queried databases and their update frequencies
+- `workflows.md` - Extended workflow examples and use cases
+
+For additional help:
+- Official documentation: https://pachterlab.github.io/gget/
+- GitHub issues: https://github.com/pachterlab/gget/issues
+- Citation: Luebbert, L. & Pachter, L. (2023). Efficient querying of genomic reference databases with gget. Bioinformatics. https://doi.org/10.1093/bioinformatics/btac836
+