Genomics Tools

Configuration File: packages/genomics_tools.json Tool Type: Local Tools Count: 20

This page contains all tools defined in the genomics_tools.json configuration file.

Available Tools

get_arboreto_info (Type: PackageTool)

Get comprehensive information about Arboreto – gene regulatory network inference

get_arboreto_info tool specification

Tool Information:

  • Name: get_arboreto_info

  • Type: PackageTool

  • Description: Get comprehensive information about Arboreto – gene regulatory network inference

Parameters:

  • info_type (string) (required) Type of information to retrieve about Arboreto

Example Usage:

query = {
    "name": "get_arboreto_info",
    "arguments": {
        "info_type": "example_value"
    }
}
result = tu.run(query)

get_cellxgene_census_info (Type: PackageTool)

Get comprehensive information about cellxgene-census – access to the CELLxGENE Census single-cell…

get_cellxgene_census_info tool specification

Tool Information:

  • Name: get_cellxgene_census_info

  • Type: PackageTool

  • Description: Get comprehensive information about cellxgene-census – access to the CELLxGENE Census single-cell data

Parameters:

  • info_type (string) (required) Type of information to retrieve about cellxgene-census

Example Usage:

query = {
    "name": "get_cellxgene_census_info",
    "arguments": {
        "info_type": "example_value"
    }
}
result = tu.run(query)

get_clair3_info (Type: PackageTool)

Get comprehensive information about Clair3 – variant calling for long-read sequencing

get_clair3_info tool specification

Tool Information:

  • Name: get_clair3_info

  • Type: PackageTool

  • Description: Get comprehensive information about Clair3 – variant calling for long-read sequencing

Parameters:

  • info_type (string) (required) Type of information to retrieve about Clair3

Example Usage:

query = {
    "name": "get_clair3_info",
    "arguments": {
        "info_type": "example_value"
    }
}
result = tu.run(query)

get_cyvcf2_info (Type: PackageTool)

Get comprehensive information about cyvcf2 – fast VCF/BCF file processing

get_cyvcf2_info tool specification

Tool Information:

  • Name: get_cyvcf2_info

  • Type: PackageTool

  • Description: Get comprehensive information about cyvcf2 – fast VCF/BCF file processing

Parameters:

  • include_examples (boolean) (optional) Whether to include usage examples and quick start guide

Example Usage:

query = {
    "name": "get_cyvcf2_info",
    "arguments": {
    }
}
result = tu.run(query)

get_deeptools_info (Type: PackageTool)

Get comprehensive information about deepTools – deep sequencing data processing

get_deeptools_info tool specification

Tool Information:

  • Name: get_deeptools_info

  • Type: PackageTool

  • Description: Get comprehensive information about deepTools – deep sequencing data processing

Parameters:

  • info_type (string) (required) Type of information to retrieve about deepTools

Example Usage:

query = {
    "name": "get_deeptools_info",
    "arguments": {
        "info_type": "example_value"
    }
}
result = tu.run(query)

get_gseapy_info (Type: PackageTool)

Get comprehensive information about GSEApy – Gene Set Enrichment Analysis in Python

get_gseapy_info tool specification

Tool Information:

  • Name: get_gseapy_info

  • Type: PackageTool

  • Description: Get comprehensive information about GSEApy – Gene Set Enrichment Analysis in Python

Parameters:

  • include_examples (boolean) (optional) Whether to include usage examples and quick start guide

Example Usage:

query = {
    "name": "get_gseapy_info",
    "arguments": {
    }
}
result = tu.run(query)

get_jcvi_info (Type: PackageTool)

Get comprehensive information about JCVI – genome assembly and comparative genomics

get_jcvi_info tool specification

Tool Information:

  • Name: get_jcvi_info

  • Type: PackageTool

  • Description: Get comprehensive information about JCVI – genome assembly and comparative genomics

Parameters:

  • info_type (string) (required) Type of information to retrieve about JCVI

Example Usage:

query = {
    "name": "get_jcvi_info",
    "arguments": {
        "info_type": "example_value"
    }
}
result = tu.run(query)

get_kipoiseq_info (Type: PackageTool)

Get information about the kipoiseq package. Kipoi sequence utilities for genomics deep learning

get_kipoiseq_info tool specification

Tool Information:

  • Name: get_kipoiseq_info

  • Type: PackageTool

  • Description: Get information about the kipoiseq package. Kipoi sequence utilities for genomics deep learning

Parameters:

No parameters required.

Example Usage:

query = {
    "name": "get_kipoiseq_info",
    "arguments": {
    }
}
result = tu.run(query)

get_poretools_info (Type: PackageTool)

Get information about the poretools package. Python package: poretools

get_poretools_info tool specification

Tool Information:

  • Name: get_poretools_info

  • Type: PackageTool

  • Description: Get information about the poretools package. Python package: poretools

Parameters:

No parameters required.

Example Usage:

query = {
    "name": "get_poretools_info",
    "arguments": {
    }
}
result = tu.run(query)

get_pybedtools_info (Type: PackageTool)

Get comprehensive information about pybedtools – Python wrapper for BEDTools

get_pybedtools_info tool specification

Tool Information:

  • Name: get_pybedtools_info

  • Type: PackageTool

  • Description: Get comprehensive information about pybedtools – Python wrapper for BEDTools

Parameters:

  • include_examples (boolean) (optional) Whether to include usage examples and quick start guide

Example Usage:

query = {
    "name": "get_pybedtools_info",
    "arguments": {
    }
}
result = tu.run(query)

get_pydeseq2_info (Type: PackageTool)

Get comprehensive information about PyDESeq2 – RNA-seq differential expression analysis

get_pydeseq2_info tool specification

Tool Information:

  • Name: get_pydeseq2_info

  • Type: PackageTool

  • Description: Get comprehensive information about PyDESeq2 – RNA-seq differential expression analysis

Parameters:

  • info_type (string) (required) Type of information to retrieve about PyDESeq2

Example Usage:

query = {
    "name": "get_pydeseq2_info",
    "arguments": {
        "info_type": "example_value"
    }
}
result = tu.run(query)

get_pyensembl_info (Type: PackageTool)

Get information about the pyensembl package. Python interface to Ensembl reference genome metadata

get_pyensembl_info tool specification

Tool Information:

  • Name: get_pyensembl_info

  • Type: PackageTool

  • Description: Get information about the pyensembl package. Python interface to Ensembl reference genome metadata

Parameters:

No parameters required.

Example Usage:

query = {
    "name": "get_pyensembl_info",
    "arguments": {
    }
}
result = tu.run(query)

get_pyfaidx_info (Type: PackageTool)

Get comprehensive information about pyfaidx – efficient FASTA file indexing and random access

get_pyfaidx_info tool specification

Tool Information:

  • Name: get_pyfaidx_info

  • Type: PackageTool

  • Description: Get comprehensive information about pyfaidx – efficient FASTA file indexing and random access

Parameters:

  • include_examples (boolean) (optional) Whether to include usage examples and quick start guide

Example Usage:

query = {
    "name": "get_pyfaidx_info",
    "arguments": {
    }
}
result = tu.run(query)

get_pyfasta_info (Type: PackageTool)

Get information about the pyfasta package. Python library for efficient random access to fasta su…

get_pyfasta_info tool specification

Tool Information:

  • Name: get_pyfasta_info

  • Type: PackageTool

  • Description: Get information about the pyfasta package. Python library for efficient random access to fasta subsequences

Parameters:

No parameters required.

Example Usage:

query = {
    "name": "get_pyfasta_info",
    "arguments": {
    }
}
result = tu.run(query)

get_pyliftover_info (Type: PackageTool)

Get comprehensive information about PyLiftover – genomic coordinate conversion between assemblies

get_pyliftover_info tool specification

Tool Information:

  • Name: get_pyliftover_info

  • Type: PackageTool

  • Description: Get comprehensive information about PyLiftover – genomic coordinate conversion between assemblies

Parameters:

  • include_examples (boolean) (optional) Whether to include usage examples and quick start guide

Example Usage:

query = {
    "name": "get_pyliftover_info",
    "arguments": {
    }
}
result = tu.run(query)

get_pyranges_info (Type: PackageTool)

Get comprehensive information about PyRanges – efficient genomic interval operations

get_pyranges_info tool specification

Tool Information:

  • Name: get_pyranges_info

  • Type: PackageTool

  • Description: Get comprehensive information about PyRanges – efficient genomic interval operations

Parameters:

  • include_examples (boolean) (optional) Whether to include usage examples and quick start guide

Example Usage:

query = {
    "name": "get_pyranges_info",
    "arguments": {
    }
}
result = tu.run(query)

get_pysam_info (Type: PackageTool)

Get comprehensive information about pysam – interface to SAM/BAM/CRAM files

get_pysam_info tool specification

Tool Information:

  • Name: get_pysam_info

  • Type: PackageTool

  • Description: Get comprehensive information about pysam – interface to SAM/BAM/CRAM files

Parameters:

  • include_examples (boolean) (optional) Whether to include usage examples and quick start guide

Example Usage:

query = {
    "name": "get_pysam_info",
    "arguments": {
    }
}
result = tu.run(query)

get_pyvcf_info (Type: PackageTool)

Get information about the pyvcf package. Python library for parsing and manipulating VCF files

get_pyvcf_info tool specification

Tool Information:

  • Name: get_pyvcf_info

  • Type: PackageTool

  • Description: Get information about the pyvcf package. Python library for parsing and manipulating VCF files

Parameters:

No parameters required.

Example Usage:

query = {
    "name": "get_pyvcf_info",
    "arguments": {
    }
}
result = tu.run(query)

get_reportlab_info (Type: PackageTool)

Get comprehensive information about ReportLab – PDF generation library

get_reportlab_info tool specification

Tool Information:

  • Name: get_reportlab_info

  • Type: PackageTool

  • Description: Get comprehensive information about ReportLab – PDF generation library

Parameters:

  • include_examples (boolean) (optional) Whether to include usage examples and quick start guide

Example Usage:

query = {
    "name": "get_reportlab_info",
    "arguments": {
    }
}
result = tu.run(query)

get_viennarna_info (Type: PackageTool)

Get comprehensive information about ViennaRNA – RNA structure prediction and analysis

get_viennarna_info tool specification

Tool Information:

  • Name: get_viennarna_info

  • Type: PackageTool

  • Description: Get comprehensive information about ViennaRNA – RNA structure prediction and analysis

Parameters:

  • include_examples (boolean) (optional) Whether to include usage examples and quick start guide

Example Usage:

query = {
    "name": "get_viennarna_info",
    "arguments": {
    }
}
result = tu.run(query)