Metadata-Version: 2.1
Name: pegs
Version: 0.5.0
Summary: Peak-set Enrichment of Gene-Sets (PEGS)
Home-page: https://github.com/fls-bioinformatics-core/pegs
Author: Mudassar Iqbal, Peter Briggs
Maintainer: Peter Briggs
Maintainer-email: peter.briggs@manchester.ac.uk
License: BSD-3-Clause
Description: **************************************
        PEGS: Peak-set Enrichment of Gene-Sets
        **************************************
        
        ``PEGS`` (**P**\ eak-set **E**\ nrichment of **G**\ ene-**S**\ ets) is
        a Python bioinformatics utility for calculating enrichments of gene
        clusters at different genomic distances from peaks.
        
        .. image:: https://readthedocs.org/projects/pegs/badge/?version=latest
           :target: https://pegs.readthedocs.io/
        
        .. image:: https://badge.fury.io/py/pegs.svg
           :target: https://pypi.python.org/pypi/pegs/
        
        .. image:: https://github.com/fls-bioinformatics-core/pegs/workflows/Python%20package/badge.svg
           :target: https://github.com/fls-bioinformatics-core/pegs/actions?query=workflow%3A%22Python+package%22
        
        * Free software: 3-Clause BSD License
        * Documentation: https://pegs.readthedocs.io/en/latest/
        * Code: https://github.com/fls-bioinformatics-core/pegs
        
        -----------
        Quick Start
        -----------
        
        It is recommended to install ``PEGS`` via ``pip`` in a virtualenv,
        for example::
        
            % virtualenv venv.pegs
            % source venv.pegs/bin/activate
            % pip install pegs
        
        This will provide the ``pegs`` and ``mk_pegs_intervals`` programs.
        
        The simplest use of ``PEGS`` is:
        
        ::
        
            pegs GENE_INTERVALS PEAKS_DIR CLUSTERS_DIR
        
        where ``GENE_INTERVALS`` is a set of reference transcription
        start sites (TSSs) for all genes, ``PEAKS_DIR`` is a directory
        containing BED files with peak-sets, and ``CLUSTERS_DIR`` is a
        directory containing files defining gene clusters.
        
        This will output a PNG heatmap and an XLXS file with the
        p-values and gene counts from the enrichment calculations.
        
        Full documentation can be found at:
        
         * https://pegs.readthedocs.io/en/latest/
        
        ---------
        Licensing
        ---------
        
        PEGS is licensed under the 3-Clause BSD License.
        
        ---------------------------------------
        Example: Mouse glucocorticoidal dataset
        ---------------------------------------
        
        *Thanks to Louise Hunter for providing this example.*
        
        An example application of ``PEGS`` is the analysis of up- and
        down-regulated glucocorticoidal targets from an RNA-seq study
        of liver samples from mice treated acutely with dexamethasone
        or vehicle (Caratti *et al.* 2018), combined with corresponding
        GR ChIP-seq and chromatin accessibility data (DNase I
        hypersensitive (DHS) regions) (Grontved *et al.* 2013 and
        Sobel *et al.* 2017 respectively), and mouse liver TAD
        boundary data (Kim *et al.* 2018).
        
        The files for these datasets are available here:
        
         * RNA-seq data:
           `1_zt6up.txt <examples/glucocorticoid_example/data/clusters/1_zt6up.txt>`_
           and `2_zt6down.txt <examples/glucocorticoid_example/data/clusters/2_zt6down.txt>`_
         * ChIP-seq and chromatin accessibility data:
           `Grontved_GR_ChIP.bed <examples/glucocorticoid_example/data/peaks/Grontved_GR_ChIP.bed>`_
           and
           `ZT6_DNase.bed <examples/glucocorticoid_example/data/peaks/ZT6_DNase.bed>`_
         * TAD boundary data:
           `mESC-TADs_mm10.txt <examples/glucocorticoid_example/data/mESC-TADs_mm10.txt>`_
        
        The ``PEGS`` analysis was performed on these data using the
        command::
        
            pegs mm10 \
              data/peaks/ data/clusters/ \
              -t data/mESC-TADs_mm10.txt \
              1000 5000 10000 50000 100000 200000 500000 1000000 5000000
        
        The resulting output files (XLSX and heatmap) can be found here:
        
         * `glucocorticoid_heatmap.png <examples/glucocorticoid_example/results/glucocorticoid_heatmap.png>`_
         * `glucocorticoid_results.xlsx <examples/glucocorticoid_example/results/glucocorticoid_results.xlsx>`_
        
        .. image:: examples/glucocorticoid_example/results/glucocorticoid_heatmap.png
        
        The analyses indicate a strong association of dexamethasone
        up-regulated genes with dexamethasone-induced GR peaks at
        distances up to 500kbp from these peaks, but no evidence of
        down-regulated genes - indicating distinct mechanisms of gene
        activation and repression by glucocorticoids. At the same time,
        there is promoter proximal enrichment for both up-and
        
        **References**
        
        * Caratti, G. *et al.* (2018) REVERBa couples the clock to hepatic
          glucocorticoid action. *J Clin Invest* **128(10)**:4454-4471
        * Grontved, L. *et al.* (2013) C/EBP maintains chromatin accessibility
          in liver and facilitates glucocorticoid receptor recruitment to
          steroid response elements. *EMBO J* **32(11)**, 1568-83
        * Kim, Y.H. *et al.* (2018) Rev-erbα dynamically modulates chromatin
          looping to control circadian gene transcription. *Science*
          **359(6381)**:1274-1277
        * Sobel, J.A. *et al.* (2017) Transcriptional regulatory logic of the
          diurnal cycle in the mouse liver. *PLoS Biol* **15(4)**: e2001069
        
        ----------------
        Acknowledgements
        ----------------
        
        Thanks to Louise Hunter for providing the mouse glucocorticoidal
        example, and to Kyle Pollina for allowing us to use the ``pegs``
        name on the Python Package Index.
        
Keywords: PEGS
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Environment :: Console
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: POSIX
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
