Bioinformatics Core Tools

Configuration File: packages/bioinformatics_core_tools.json Tool Type: Local Tools Count: 37

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

Available Tools

get_arxiv_info (Type: PackageTool)

Get comprehensive information about arxiv – access to arXiv preprint repository

get_arxiv_info tool specification

Tool Information:

  • Name: get_arxiv_info

  • Type: PackageTool

  • Description: Get comprehensive information about arxiv – access to arXiv preprint repository

Parameters:

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

Example Usage:

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

get_biopython_info (Type: PackageTool)

Get comprehensive information about Biopython – powerful tools for computational molecular biolog…

get_biopython_info tool specification

Tool Information:

  • Name: get_biopython_info

  • Type: PackageTool

  • Description: Get comprehensive information about Biopython – powerful tools for computational molecular biology and bioinformatics

Parameters:

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

Example Usage:

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

get_bioservices_info (Type: PackageTool)

Get information about the bioservices package. Python package: bioservices

get_bioservices_info tool specification

Tool Information:

  • Name: get_bioservices_info

  • Type: PackageTool

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

Parameters:

No parameters required.

Example Usage:

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

get_biotite_info (Type: PackageTool)

Get comprehensive information about Biotite – comprehensive computational molecular biology library

get_biotite_info tool specification

Tool Information:

  • Name: get_biotite_info

  • Type: PackageTool

  • Description: Get comprehensive information about Biotite – comprehensive computational molecular biology library

Parameters:

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

Example Usage:

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

get_cryosparc_tools_info (Type: PackageTool)

Get comprehensive information about cryosparc-tools – interface to CryoSPARC cryo-EM processing

get_cryosparc_tools_info tool specification

Tool Information:

  • Name: get_cryosparc_tools_info

  • Type: PackageTool

  • Description: Get comprehensive information about cryosparc-tools – interface to CryoSPARC cryo-EM processing

Parameters:

  • info_type (string) (required) Type of information to retrieve about cryosparc-tools

Example Usage:

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

get_dendropy_info (Type: PackageTool)

Get information about the dendropy package. Python package: dendropy

get_dendropy_info tool specification

Tool Information:

  • Name: get_dendropy_info

  • Type: PackageTool

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

Parameters:

No parameters required.

Example Usage:

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

get_ete3_info (Type: PackageTool)

Get information about the ete3 package. Python package: ete3

get_ete3_info tool specification

Tool Information:

  • Name: get_ete3_info

  • Type: PackageTool

  • Description: Get information about the ete3 package. Python package: ete3

Parameters:

No parameters required.

Example Usage:

query = {
    "name": "get_ete3_info",
    "arguments": {
    }
}
result = tu.run(query)

get_fanc_info (Type: PackageTool)

Get comprehensive information about FAN-C – framework for analyzing nuclear contacts

get_fanc_info tool specification

Tool Information:

  • Name: get_fanc_info

  • Type: PackageTool

  • Description: Get comprehensive information about FAN-C – framework for analyzing nuclear contacts

Parameters:

  • info_type (string) (required) Type of information to retrieve about FAN-C

Example Usage:

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

get_flask_info (Type: PackageTool)

Get comprehensive information about Flask - a lightweight WSGI web application framework

get_flask_info tool specification

Tool Information:

  • Name: get_flask_info

  • Type: PackageTool

  • Description: Get comprehensive information about Flask - a lightweight WSGI web application framework

Parameters:

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

Example Usage:

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

get_flowio_info (Type: PackageTool)

Get comprehensive information about FlowIO – FCS file I/O for flow cytometry

get_flowio_info tool specification

Tool Information:

  • Name: get_flowio_info

  • Type: PackageTool

  • Description: Get comprehensive information about FlowIO – FCS file I/O for flow cytometry

Parameters:

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

Example Usage:

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

get_flowkit_info (Type: PackageTool)

Get comprehensive information about FlowKit – flow cytometry analysis toolkit

get_flowkit_info tool specification

Tool Information:

  • Name: get_flowkit_info

  • Type: PackageTool

  • Description: Get comprehensive information about FlowKit – flow cytometry analysis toolkit

Parameters:

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

Example Usage:

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

get_gget_info (Type: PackageTool)

Get comprehensive information about gget – genomics command-line tool and Python package

get_gget_info tool specification

Tool Information:

  • Name: get_gget_info

  • Type: PackageTool

  • Description: Get comprehensive information about gget – genomics command-line tool and Python package

Parameters:

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

Example Usage:

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

get_googlesearch_python_info (Type: PackageTool)

Get comprehensive information about googlesearch-python – Google search automation

get_googlesearch_python_info tool specification

Tool Information:

  • Name: get_googlesearch_python_info

  • Type: PackageTool

  • Description: Get comprehensive information about googlesearch-python – Google search automation

Parameters:

  • info_type (string) (required) Type of information to retrieve about googlesearch-python

Example Usage:

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

get_khmer_info (Type: PackageTool)

Get comprehensive information about khmer – nucleotide sequence k-mer analysis

get_khmer_info tool specification

Tool Information:

  • Name: get_khmer_info

  • Type: PackageTool

  • Description: Get comprehensive information about khmer – nucleotide sequence k-mer analysis

Parameters:

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

Example Usage:

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

get_lifelines_info (Type: PackageTool)

Get comprehensive information about lifelines – survival analysis in Python

get_lifelines_info tool specification

Tool Information:

  • Name: get_lifelines_info

  • Type: PackageTool

  • Description: Get comprehensive information about lifelines – survival analysis in Python

Parameters:

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

Example Usage:

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

get_loompy_info (Type: PackageTool)

Get comprehensive information about loompy – efficient storage for large omics datasets

get_loompy_info tool specification

Tool Information:

  • Name: get_loompy_info

  • Type: PackageTool

  • Description: Get comprehensive information about loompy – efficient storage for large omics datasets

Parameters:

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

Example Usage:

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

get_mageck_info (Type: PackageTool)

Get comprehensive information about MAGeCK – CRISPR screen analysis toolkit

get_mageck_info tool specification

Tool Information:

  • Name: get_mageck_info

  • Type: PackageTool

  • Description: Get comprehensive information about MAGeCK – CRISPR screen analysis toolkit

Parameters:

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

Example Usage:

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

get_msprime_info (Type: PackageTool)

Get comprehensive information about msprime – coalescent simulation framework

get_msprime_info tool specification

Tool Information:

  • Name: get_msprime_info

  • Type: PackageTool

  • Description: Get comprehensive information about msprime – coalescent simulation framework

Parameters:

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

Example Usage:

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

get_networkx_info (Type: PackageTool)

Get comprehensive information about NetworkX – network analysis library

get_networkx_info tool specification

Tool Information:

  • Name: get_networkx_info

  • Type: PackageTool

  • Description: Get comprehensive information about NetworkX – network analysis library

Parameters:

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

Example Usage:

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

get_numba_info (Type: PackageTool)

Get comprehensive information about Numba – JIT compiler for Python

get_numba_info tool specification

Tool Information:

  • Name: get_numba_info

  • Type: PackageTool

  • Description: Get comprehensive information about Numba – JIT compiler for Python

Parameters:

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

Example Usage:

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

get_pdbfixer_info (Type: PackageTool)

Get comprehensive information about PDBFixer – protein structure preparation tool

get_pdbfixer_info tool specification

Tool Information:

  • Name: get_pdbfixer_info

  • Type: PackageTool

  • Description: Get comprehensive information about PDBFixer – protein structure preparation tool

Parameters:

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

Example Usage:

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

get_plip_info (Type: PackageTool)

Get comprehensive information about PLIP – protein-ligand interaction profiler

get_plip_info tool specification

Tool Information:

  • Name: get_plip_info

  • Type: PackageTool

  • Description: Get comprehensive information about PLIP – protein-ligand interaction profiler

Parameters:

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

Example Usage:

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

get_poliastro_info (Type: PackageTool)

Get comprehensive information about poliastro – astrodynamics library

get_poliastro_info tool specification

Tool Information:

  • Name: get_poliastro_info

  • Type: PackageTool

  • Description: Get comprehensive information about poliastro – astrodynamics library

Parameters:

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

Example Usage:

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

get_prody_info (Type: PackageTool)

Get comprehensive information about ProDy – protein dynamics analysis

get_prody_info tool specification

Tool Information:

  • Name: get_prody_info

  • Type: PackageTool

  • Description: Get comprehensive information about ProDy – protein dynamics analysis

Parameters:

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

Example Usage:

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

get_pybigwig_info (Type: PackageTool)

Get comprehensive information about pyBigWig – BigWig file access in Python

get_pybigwig_info tool specification

Tool Information:

  • Name: get_pybigwig_info

  • Type: PackageTool

  • Description: Get comprehensive information about pyBigWig – BigWig file access in Python

Parameters:

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

Example Usage:

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

get_pykalman_info (Type: PackageTool)

Get comprehensive information about PyKalman – Kalman filtering and smoothing

get_pykalman_info tool specification

Tool Information:

  • Name: get_pykalman_info

  • Type: PackageTool

  • Description: Get comprehensive information about PyKalman – Kalman filtering and smoothing

Parameters:

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

Example Usage:

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

get_pymassspec_info (Type: PackageTool)

Get comprehensive information about PyMassSpec – mass spectrometry data analysis

get_pymassspec_info tool specification

Tool Information:

  • Name: get_pymassspec_info

  • Type: PackageTool

  • Description: Get comprehensive information about PyMassSpec – mass spectrometry data analysis

Parameters:

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

Example Usage:

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

get_pymed_info (Type: PackageTool)

Get comprehensive information about PyMed – PubMed access in Python

get_pymed_info tool specification

Tool Information:

  • Name: get_pymed_info

  • Type: PackageTool

  • Description: Get comprehensive information about PyMed – PubMed access in Python

Parameters:

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

Example Usage:

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

get_pypdf2_info (Type: PackageTool)

Get comprehensive information about PyPDF2 – PDF manipulation library

get_pypdf2_info tool specification

Tool Information:

  • Name: get_pypdf2_info

  • Type: PackageTool

  • Description: Get comprehensive information about PyPDF2 – PDF manipulation library

Parameters:

  • info_type (string) (required) Type of information to retrieve about PyPDF2

Example Usage:

query = {
    "name": "get_pypdf2_info",
    "arguments": {
        "info_type": "example_value"
    }
}
result = tu.run(query)

get_pyscreener_info (Type: PackageTool)

Get comprehensive information about PyScreener – high-throughput virtual screening in Python

get_pyscreener_info tool specification

Tool Information:

  • Name: get_pyscreener_info

  • Type: PackageTool

  • Description: Get comprehensive information about PyScreener – high-throughput virtual screening in Python

Parameters:

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

Example Usage:

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

get_pytdc_info (Type: PackageTool)

Get comprehensive information about PyTDC – Therapeutics Data Commons in Python

get_pytdc_info tool specification

Tool Information:

  • Name: get_pytdc_info

  • Type: PackageTool

  • Description: Get comprehensive information about PyTDC – Therapeutics Data Commons in Python

Parameters:

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

Example Usage:

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

get_requests_info (Type: PackageTool)

Get comprehensive information about Requests - Python HTTP library for humans

get_requests_info tool specification

Tool Information:

  • Name: get_requests_info

  • Type: PackageTool

  • Description: Get comprehensive information about Requests - Python HTTP library for humans

Parameters:

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

Example Usage:

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

get_ruptures_info (Type: PackageTool)

Get comprehensive information about ruptures – change point detection library

get_ruptures_info tool specification

Tool Information:

  • Name: get_ruptures_info

  • Type: PackageTool

  • Description: Get comprehensive information about ruptures – change point detection library

Parameters:

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

Example Usage:

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

get_scholarly_info (Type: PackageTool)

Get comprehensive information about scholarly – Google Scholar data retrieval

get_scholarly_info tool specification

Tool Information:

  • Name: get_scholarly_info

  • Type: PackageTool

  • Description: Get comprehensive information about scholarly – Google Scholar data retrieval

Parameters:

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

Example Usage:

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

get_scikit_bio_info (Type: PackageTool)

Get comprehensive information about scikit-bio – bioinformatics library built on scientific Pytho…

get_scikit_bio_info tool specification

Tool Information:

  • Name: get_scikit_bio_info

  • Type: PackageTool

  • Description: Get comprehensive information about scikit-bio – bioinformatics library built on scientific Python stack

Parameters:

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

Example Usage:

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

get_trackpy_info (Type: PackageTool)

Get comprehensive information about trackpy – particle tracking toolkit for Python

get_trackpy_info tool specification

Tool Information:

  • Name: get_trackpy_info

  • Type: PackageTool

  • Description: Get comprehensive information about trackpy – particle tracking toolkit for Python

Parameters:

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

Example Usage:

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

get_tskit_info (Type: PackageTool)

Get comprehensive information about tskit – tree sequence toolkit for population genetics

get_tskit_info tool specification

Tool Information:

  • Name: get_tskit_info

  • Type: PackageTool

  • Description: Get comprehensive information about tskit – tree sequence toolkit for population genetics

Parameters:

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

Example Usage:

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