gget

Name: gget
Author: K-Dense-AI

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How to install gget?

k-dense-ai/scientific-agent-skills/gget

$npx -y skills add K-Dense-AI/scientific-agent-skills --skill gget

Installs into the current project.

Summary

Fast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST/BLAT, viral sequence downloads, AlphaFold structures, enrichment analysis, OpenTargets, COSMIC, CELLxGENE, and 8cube mouse specificity/expression data. Best for interactive exploratio

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SKILL.md

1	# gget
2
3	## Overview
4
5	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, viral sequences, expression data, disease associations, and mouse tissue/cell specificity metrics through a consistent interface. Most gget modules work both as command-line tools and as Python functions.
6
7	Important: The databases queried by gget are continuously updated, which sometimes changes their structure. Guidance here targets gget 0.30.5 (PyPI current as of 2026-06-07). For reproducible work, pin `gget==0.30.5`; for broken upstream database adapters, update gget after checking release notes.
8
9	## Installation
10
11	Install gget in a clean virtual environment to avoid conflicts:
12
13	```bash
14	# Reproducible install targeting this skill
15	uv venv .venv
16	source .venv/bin/activate
17	uv pip install "gget==0.30.5"
18
19	# In Python/Jupyter
20	import gget
21	```
22
23	## Quick Start
24
25	Basic usage pattern for all modules:
26
27	```bash
28	# Command-line
29	gget <module> [arguments] [options]
30
31	# Python
32	gget.module(arguments, options)
33	```
34
35	Most modules return:
36	- Command-line: JSON (default) or CSV with `-csv` flag
37	- Python: DataFrame or dictionary
38
39	Common flags across modules:
40	- `-o/--out`: Save results to file
41	- `-q/--quiet`: Suppress progress information
42	- `-csv`: Return CSV format (command-line only)
43
44	Python argument names generally match long CLI options without leading dashes. For example, `--census_version` becomes `census_version=...`. Use `gget <module> --help` for the exact current signature.
45
46	## Module Categories
47
48	### 1. Reference & Gene Information
49
50	#### gget ref - Reference Genome Downloads
51
52	Retrieve download links and metadata for Ensembl reference genomes.
53
54	Parameters:
55	- `species`: Genus_species format (e.g., 'homo_sapiens', 'mus_musculus'). Shortcuts: 'human', 'mouse'
56	- `-w/--which`: Specify return types as comma-separated CLI values or Python list (gtf, cdna, dna, cds, cdrna, pep). Default: all
57	- `-r/--release`: Ensembl release number (default: latest)
58	- `-od/--out_dir`: Directory for downloaded files
59	- `-l/--list_species`: List available vertebrate species
60	- `-liv/--list_iv_species`: List available invertebrate species
61	- `-ftp`: Return only FTP links
62	- `-d/--download`: Download files (requires curl)
63
64	Examples:
65	```bash
66	# List available species
67	gget ref --list_species
68
69	# Get all reference files for human
70	gget ref homo_sapiens
71
72	# Download GTF and cDNA files for mouse
73	gget ref -w gtf,cdna -d mouse
74	```
75
76	```python
77	# Python
78	gget.ref("homo_sapiens")
79	gget.ref("mus_musculus", which=["gtf", "cdna"], download=True)
80	```
81
82	#### gget search - Gene Search
83
84	Locate genes by name, description, and Ensembl synonyms across species.
85
86	Parameters:
87	- `searchwords`: One or more search terms (case-insensitive)
88	- `-s/--species`: Target species (e.g., 'homo_sapiens', 'mouse')
89	- `-r/--release`: Ensembl release number
90	- `-t/--id_type`: Return 'gene' (default) or 'transcript'
91	- `-ao/--andor`: 'or' (default) finds ANY searchword; 'and' requires ALL
92	- `-l/--limit`: Maximum results to return
93	- `wrap_text`: Python-only display helper for wide DataFrames
94
95	Returns: ensembl_id, gene_name, ensembl_description, ext_ref_description, biotype, URL
96
97	Examples:
98	```bash
99	# Search for GABA-related genes in human
100	gget search -s human gaba gamma-aminobutyric
101
102	# Find specific gene, require all terms
103	gget search -s mouse -ao and pax7 transcription
104	```
105
106	```python
107	# Python
108	gget.search(["gaba", "gamma-aminobutyric"], species="homo_sapiens")
109	```
110
111	#### gget info - Gene/Transcript Information
112
113	Retrieve comprehensive gene and transcript metadata from Ensembl, UniProt, and NCBI.
114
115	Parameters:
116	- `ens_ids`: One or more Ensembl IDs (also supports WormBase, Flybase IDs). Limit: ~1000 IDs
117	- `-n/--ncbi`: Disable NCBI data retrieval
118	- `-u/--uniprot`: Disable UniProt data retrieval
119	- `-pdb`: Include PDB identifiers (increases runtime)
120
121	Returns: UniProt ID, NCBI gene ID, primary gene name, synonyms, protein names, descriptions, biotype, canonical transcript
122
123	Examples:
124	```bash
125	# Get info for multiple genes
126	gget info ENSG00000034713

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gget

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View on GitHub

How to install gget?

k-dense-ai/scientific-agent-skills/gget

$npx -y skills add K-Dense-AI/scientific-agent-skills --skill gget

Installs into the current project.

Summary

Files · 1

View on GitHub

SKILL.md

1	# gget
2
3	## Overview
4
5	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, viral sequences, expression data, disease associations, and mouse tissue/cell specificity metrics through a consistent interface. Most gget modules work both as command-line tools and as Python functions.
6
7	Important: The databases queried by gget are continuously updated, which sometimes changes their structure. Guidance here targets gget 0.30.5 (PyPI current as of 2026-06-07). For reproducible work, pin `gget==0.30.5`; for broken upstream database adapters, update gget after checking release notes.
8
9	## Installation
10
11	Install gget in a clean virtual environment to avoid conflicts:
12
13	```bash
14	# Reproducible install targeting this skill
15	uv venv .venv
16	source .venv/bin/activate
17	uv pip install "gget==0.30.5"
18
19	# In Python/Jupyter
20	import gget
21	```
22
23	## Quick Start
24
25	Basic usage pattern for all modules:
26
27	```bash
28	# Command-line
29	gget <module> [arguments] [options]
30
31	# Python
32	gget.module(arguments, options)
33	```
34
35	Most modules return:
36	- Command-line: JSON (default) or CSV with `-csv` flag
37	- Python: DataFrame or dictionary
38
39	Common flags across modules:
40	- `-o/--out`: Save results to file
41	- `-q/--quiet`: Suppress progress information
42	- `-csv`: Return CSV format (command-line only)
43
44	Python argument names generally match long CLI options without leading dashes. For example, `--census_version` becomes `census_version=...`. Use `gget <module> --help` for the exact current signature.
45
46	## Module Categories
47
48	### 1. Reference & Gene Information
49
50	#### gget ref - Reference Genome Downloads
51
52	Retrieve download links and metadata for Ensembl reference genomes.
53
54	Parameters:
55	- `species`: Genus_species format (e.g., 'homo_sapiens', 'mus_musculus'). Shortcuts: 'human', 'mouse'
56	- `-w/--which`: Specify return types as comma-separated CLI values or Python list (gtf, cdna, dna, cds, cdrna, pep). Default: all
57	- `-r/--release`: Ensembl release number (default: latest)
58	- `-od/--out_dir`: Directory for downloaded files
59	- `-l/--list_species`: List available vertebrate species
60	- `-liv/--list_iv_species`: List available invertebrate species
61	- `-ftp`: Return only FTP links
62	- `-d/--download`: Download files (requires curl)
63
64	Examples:
65	```bash
66	# List available species
67	gget ref --list_species
68
69	# Get all reference files for human
70	gget ref homo_sapiens
71
72	# Download GTF and cDNA files for mouse
73	gget ref -w gtf,cdna -d mouse
74	```
75
76	```python
77	# Python
78	gget.ref("homo_sapiens")
79	gget.ref("mus_musculus", which=["gtf", "cdna"], download=True)
80	```
81
82	#### gget search - Gene Search
83
84	Locate genes by name, description, and Ensembl synonyms across species.
85
86	Parameters:
87	- `searchwords`: One or more search terms (case-insensitive)
88	- `-s/--species`: Target species (e.g., 'homo_sapiens', 'mouse')
89	- `-r/--release`: Ensembl release number
90	- `-t/--id_type`: Return 'gene' (default) or 'transcript'
91	- `-ao/--andor`: 'or' (default) finds ANY searchword; 'and' requires ALL
92	- `-l/--limit`: Maximum results to return
93	- `wrap_text`: Python-only display helper for wide DataFrames
94
95	Returns: ensembl_id, gene_name, ensembl_description, ext_ref_description, biotype, URL
96
97	Examples:
98	```bash
99	# Search for GABA-related genes in human
100	gget search -s human gaba gamma-aminobutyric
101
102	# Find specific gene, require all terms
103	gget search -s mouse -ao and pax7 transcription
104	```
105
106	```python
107	# Python
108	gget.search(["gaba", "gamma-aminobutyric"], species="homo_sapiens")
109	```
110
111	#### gget info - Gene/Transcript Information
112
113	Retrieve comprehensive gene and transcript metadata from Ensembl, UniProt, and NCBI.
114
115	Parameters:
116	- `ens_ids`: One or more Ensembl IDs (also supports WormBase, Flybase IDs). Limit: ~1000 IDs
117	- `-n/--ncbi`: Disable NCBI data retrieval
118	- `-u/--uniprot`: Disable UniProt data retrieval
119	- `-pdb`: Include PDB identifiers (increases runtime)
120
121	Returns: UniProt ID, NCBI gene ID, primary gene name, synonyms, protein names, descriptions, biotype, canonical transcript
122
123	Examples:
124	```bash
125	# Get info for multiple genes
126	gget info ENSG00000034713

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