rnachipintegrator

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

https://github.com/fls-bioinformatics-core/rnachipintegrator

Repository

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

README.rst

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.

Owner

Citation (CITATION.cff)

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: RnaChipIntegrator
version: 3.0.0
type: software
message: >-
  If you use this software, please cite it using the
  metadata from this file.
authors:
  - given-names: Peter
    family-names: Briggs
    email: peter.briggs@manchester.ac.uk
    affiliation: University of Manchester
  - given-names: Ian
    family-names: Donaldson
    affiliation: University of Manchester
    email: ian.donaldson@manchester.ac.uk
  - given-names: Leo
    family-names: Zeef
    email: leo.zeef@manchester.ac.uk
    affiliation: University of Manchester
identifiers:
  - description: "Archived snapshots of all versions of RnaChipIntegrator"
    type: doi
    value: 10.5281/zenodo.592255
  - description: "Archived snapshot of version 3.0.0 of RnaChipIntegrator"
    type: doi
    value: 10.5281/zenodo.10623997
  - description: "Archived snapshot of version 1.0.2 of RnaChipIntegrator"
    type: doi
    value: 10.5281/zenodo.60362
repository-code: >-
  https://github.com/fls-bioinformatics-core/RnaChipIntegrator
url: >-
  https://rnachipintegrator.readthedocs.io/en/latest/index.html
abstract: >-
  RnaChipIntegrator is a software 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.

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