CHANGES IN VERSION 1.0.17
-------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o recount_url now includes the URLs for the GTEx bigWig files.

CHANGES IN VERSION 1.0.14
-------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o coverage_matrix() now returns a RangedSummarizedExperiment object. This
        matches the behavior of recount.bwtool::coverage_matrix_bwtool() and
        is more consistent with the use of RSE objects in recount.


CHANGES IN VERSION 1.0.12
-------------------------

BUG FIXES

    o coverage_matrix()'s helper function .read_pheno() was failing for some
        projects.

CHANGES IN VERSION 1.0.11
-------------------------

BUG FIXES

    o Fixed a bug in the counts in coverage_matrix(). They were being 
        incorrectly multiplied by 100.

CHANGES IN VERSION 1.0.8
------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o The gene and exon counts are now based on Gencode v25 instead of
        UCSC knownGene hg38.


CHANGES IN VERSION 1.0.7
------------------------

BUG FIXES

    o Updated snaptron_query() to comply with recent changes in Snaptron.


CHANGES IN VERSION 1.0.4
------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Updated the package so you can now access TCGA data. Now there's over
        8 terabytes of data available in the recount project!


CHANGES IN VERSION 1.0.2
------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Merged in changes from the devel branch (versions 1.1.1 and 1.1.2) to
        the release branch (v1.0.2)
    o snaptron_query() now can query GTEx and TCGA data.

CHANGES IN VERSION 1.0.1
------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Snaptron changed from stingray.cs.jhu.edu:8090 to snaptron.cs.jhu.edu so
        snaptron_query() has been changed accordingly.


CHANGES IN VERSION 0.99.30
--------------------------

NEW FEATURES

    o Added the function snaptron_query() which queries Intropolis via Snaptron
        to find if an exon-exon junction is present in the data.


CHANGES IN VERSION 0.99.29
--------------------------

BUF FIXES

    o Fixed an bug in the vignette. Thanks to Michael Love for noticing it!


CHANGES IN VERSION 0.99.0
-------------------------

NEW FEATURES

    o Created the package skeleton for recount
    o Added the function reproduce_ranges() for re-creating the gene or exon
        level information used in the recount project.
    o Added the function abstract_search() for identifying SRA projects of
        interest by searching the abstracts.
    o Added the function browse_study() for opening a browser tab for further
        exploring a project.
    o Added the function download_study() for downloading the data from the
        recount project.
    o Added the function scale_counts() for properly scaling the counts before
        performing a differential expression analysis with the
        RangedSummarizedExperiment objects hosted in the recount project.
    o Added the function expressed_regions() for defining the expressed regions
        in a chromosome for a given SRA study.
    o Added the function coverage_matrix() for computing the coverage matrix
        based on the regions of interest for a given SRA study.
    o Added the function geo_info() for obtaining sample information from GEO.
    o Added the function find_geo() for finding the GEO accession id given a
        SRA run accession (id). This function will be useful for SRA projects
        that did not have GEO entries at the time recount's data was created.
    o Added the function geo_characteristics() for building a data.frame from
        geo_info()'s results for the characteristics.
    o Added the function all_metadata() which downloads all the phenotype data
        for all projects. This function can be useful for identifying projects
        and/or samples of interests.