RnaChipIntegrator: analysis of genes with peak data
===================================================
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``RnaChipIntegrator`` is a utility that performs integrated analyses
of 'gene' data (a set of genes or other genomic features) with 'peak'
data (a set of regions, for example ChIP peaks) to identify the genes
nearest to each peak, and vice versa.
The program was originally written specifically for ChIP-Seq and RNA-Seq
data but works equally well for ChIP-chip and microarray expression data,
and can also be used to integrate any set of genomic features (e.g.
canonical genes, CpG islands) with peak data.
Quick Start
***********
Install the latest version of the program from the Python Package Index
(PyPI)::
pip install RnaChipIntegrator
The simplest use of the program is::
RnaChipIntegrator GENES PEAKS
where ``GENES`` and ``PEAKS`` are tab-delimited files containing the
'gene' and 'peak' data respectively.
This will output two files with the nearest genes for each peak
("peak-centric" analysis), and the nearest peaks for each gene
("gene-centric" analysis).
Full documentation can be found at:
* http://rnachipintegrator.readthedocs.io/en/latest/
Licensing
*********
This software is licensed under the Artistic License 2.0.
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"description": "RnaChipIntegrator: analysis of genes with peak data\n===================================================\n\n.. image:: https://readthedocs.org/projects/rnachipintegrator/badge/?version=latest\n :target: https://rnachipintegrator.readthedocs.io\n\n.. image:: https://badge.fury.io/py/RnaChipIntegrator.svg\n :target: https://pypi.python.org/pypi/rnachipintegrator/\n\n.. image:: https://github.com/fls-bioinformatics-core/RnaChipIntegrator/workflows/Python%20CI/badge.svg\n :target: https://github.com/fls-bioinformatics-core/RnaChipIntegrator/actions?query=workflow%3A%22Python+CI%22\n\n``RnaChipIntegrator`` is a utility that performs integrated analyses\nof 'gene' data (a set of genes or other genomic features) with 'peak'\ndata (a set of regions, for example ChIP peaks) to identify the genes\nnearest to each peak, and vice versa.\n\nThe program was originally written specifically for ChIP-Seq and RNA-Seq\ndata but works equally well for ChIP-chip and microarray expression data,\nand can also be used to integrate any set of genomic features (e.g.\ncanonical genes, CpG islands) with peak data.\n\nQuick Start\n***********\n\nInstall the latest version of the program from the Python Package Index\n(PyPI)::\n\n pip install RnaChipIntegrator\n\nThe simplest use of the program is::\n\n RnaChipIntegrator GENES PEAKS\n\nwhere ``GENES`` and ``PEAKS`` are tab-delimited files containing the\n'gene' and 'peak' data respectively.\n\nThis will output two files with the nearest genes for each peak\n(\"peak-centric\" analysis), and the nearest peaks for each gene\n(\"gene-centric\" analysis).\n\nFull documentation can be found at:\n\n * http://rnachipintegrator.readthedocs.io/en/latest/\n\nLicensing\n*********\n\nThis software is licensed under the Artistic License 2.0.\n",
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