Changes in version 1.13.2                        

SIGNIFICANT USER-VISIBLE CHANGES

  - Documentation website is now available at
    http://leekgroup.github.io/recount/. It gets updated with every
    commit on the master branch (bioc-devel) using GitHub Actions and
    pkgdown.

                       Changes in version 1.13.1                        

  - Mention in reproduce_ranges() the link to
    https://support.bioconductor.org/p/126148/#126173 which shows how to
    update the gene symbols in the RSE objects in recount.

                       Changes in version 1.11.14                       

  - Added a NEWS.md file to track changes to the package.

                       Changes in version 1.11.13                       

NEW FEATURES

  - Added the function getTPM() as discussed in
    https://support.bioconductor.org/p/124265 and based on Sonali Arora
    et al https://www.biorxiv.org/content/10.1101/445601v2.

                       Changes in version 1.11.12                       

BUG FIXES

  - Now geo_characteristics() can deal with the scenario reported at
    https://support.bioconductor.org/p/116480/ by @Jacques.van-Helden.

                       Changes in version 1.11.7                        

SIGNIFICANT USER-VISIBLE CHANGES

  - Renamed .load_install() as .load_check() as this function now only
    checks that the package(s) was installed and returns an error if
    missing. The error shows the user how to install the package(s) they
    are missing instead of installing them automatically. This complies
    with Marcel Ramos' request at
    https://github.com/leekgroup/recount/issues/14.

                       Changes in version 1.11.4                        

NEW FEATURES

  - Added the function download_retry() based on
    http://bioconductor.org/developers/how-to/web-query/ such that
    download_file() and other recount functions will re-try to download
    a file 3 times before giving up. This should help reduce the number
    of occasional failed Bioconductor nightly checks.

                        Changes in version 1.9.7                        

SIGNIFICANT USER-VISIBLE CHANGES

  - Cleaned up the documentation of add_metadata() and changed the
    default source from recount_brain_v1 to recount_brain_v2.

                        Changes in version 1.9.6                        

NEW FEATURES

  - citation('recount')[5] now lists the recount-brain bioRxiv pre-print
    citation information.

                        Changes in version 1.9.5                        

NEW FEATURES

  - We have now released the FANTOM-CAT/recount2 RSE files which you can
    access now through download_study(type = 'rse-fc'). See Imada EL,
    Sanchez DF, et al, bioRxiv, 2019
    https://www.biorxiv.org/content/10.1101/659490v1 for more
    information.

                        Changes in version 1.9.4                        

BUG FIXES

  - I made the example code for geo_characteristics() more robust since
    currently rentrez can occasionally fails.

                        Changes in version 1.9.3                        

NEW FEATURES

  - Add ORCID's following changes at
    http://bioconductor.org/developers/package-guidelines/#description

                        Changes in version 1.9.2                        

BUG FIXES

  - Added the argument async to snaptron_query() which can be set to
    FALSE to address the issue reported at
    https://github.com/ChristopherWilks/snaptron/issues/11

                        Changes in version 1.7.7                        

BUG FIXES

  - Updated reproduce_ranges() to match the URL change in Gencode from
    ftp://ftp.sanger.ac.uk to ftp://ftp.ebi.ac.uk

                        Changes in version 1.7.5                        

SIGNIFICANT USER-VISIBLE CHANGES

  - add_metadata() can now download the recount_brain_v2 data.

                        Changes in version 1.7.4                        

BUG FIXES

  - Fix a NOTE about RefManageR.

                        Changes in version 1.7.3                        

SIGNIFICANT USER-VISIBLE CHANGES

  - Use BiocManager

                        Changes in version 1.7.2                        

BUG FIXES

  - Fix a unit test.

                        Changes in version 1.7.1                        

SIGNIFICANT USER-VISIBLE CHANGES

  - rse_tx URLs now point to v2 to reflect recent changes by Fu et al.

                       Changes in version 1.5.11                        

BUG FIXES

  - Change some examples to dontrun and improve the code that cleans up
    after the tests. This should reduce the size of files left in tmp
    although they didn't seem too big to begin with.

                        Changes in version 1.5.9                        

SIGNIFICANT USER-VISIBLE CHANGES

  - The functions add_metadata() and add_predictions() now return the
    sample metadata or predictions when the rse argument is missing.

                        Changes in version 1.5.6                        

NEW FEATURES

  - Added the function add_metadata() which can be used to append
    curated metadata to a recount rse object. Currently, add_metadata()
    only supports the recount_brain_v1 data available at
    http://lieberinstitute.github.io/recount-brain/ and to be further
    described in Razmara et al, in prep, 2018.

                        Changes in version 1.5.5                        

BUG FIXES

  - Fix doc link in geo_characteristics() which affected the Windows
    build machines.

                        Changes in version 1.5.4                        

BUG FIXES

  - Fix a unit test for download_study(), add another test for the
    versions, and fix a NOTE in R CMD check.

                        Changes in version 1.5.3                        

NEW FEATURES

  - download_study() can now download the transcript counts
    (rse_tx.RData) files. The transcript estimation is described in Fu
    et al, 2018.

SIGNIFICANT USER-VISIBLE CHANGES

  - download_study() now has a version parameter (defaults to 2). This
    argument controls which version of the files to download based on
    the change on how exons were defined. Version 1 are reduced exons
    while version 2 are disjoint exons as described in further detail in
    the documentation tab of the recount website
    https://jhubiostatistics.shinyapps.io/recount/.
  - recount_url and the example rse_gene_SRP009615 have been updated to
    match the changes in version 2.

                       Changes in version 1.3.13                        

BUG FIXES

  - Changed reproduce_ranges() since disjoint exons are more useful than
    reduced exons for downstream analyses.

                       Changes in version 1.3.12                        

NEW FEATURES

  - Added the function read_counts().

                        Changes in version 1.3.9                        

SIGNIFICANT USER-VISIBLE CHANGES

  - Added citations for
    https://www.biorxiv.org/content/early/2017/06/03/145656 and
    https://f1000research.com/articles/6-1558/v1 as well as mentions to
    them in the vignette.

                        Changes in version 1.3.7                        

SIGNIFICANT USER-VISIBLE CHANGES

  - add_predictions() was bumped to version 0.0.05

                        Changes in version 1.3.5                        

SIGNIFICANT USER-VISIBLE CHANGES

  - Vignette now uses the new BiocStyle::html_document that was recently
    released.

                        Changes in version 1.3.2                        

NEW FEATURES

  - coverage_matrix() now has two new arguments: scale and round. Use
    scale = FALSE to get raw coverage counts, which you can then scale
    with scale_counts(). scale is set to TRUE by default, so the counts
    are scaled to a library size of 40 million reads. round is set to
    FALSE by default, but can be set to TRUE if you want to get integer
    counts, just as in the default of scale_counts().

                        Changes in version 1.3.1                        

SIGNIFICANT USER-VISIBLE CHANGES

  - Changed the default version argument of add_predictions() to latest.
    Internally, that's still 0.0.03.

                       Changes in version 1.1.27                        

NEW FEATURES

  - Added the add_predictions() function which appends the predicted
    phenotypes to a RSE object downloaded with recount. The phenotypes
    were predicted by Shannon Ellis et al, 2017 (citation coming up
    soon!).

                       Changes in version 1.1.26                        

SIGNIFICANT USER-VISIBLE CHANGES

  - Changed the citation now that the recount2 paper has been published
    at http://www.nature.com/nbt/journal/v35/n4/full/nbt.3838.html.

                       Changes in version 1.1.25                        

NEW FEATURES

  - Added the function getRPKM() which can be used with
    RangedSummarizedExperiment objects from recount and from other
    sources.

                       Changes in version 1.1.24                        

SIGNIFICANT USER-VISIBLE CHANGES

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

                       Changes in version 1.1.19                        

SIGNIFICANT USER-VISIBLE CHANGES

  - 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 1.1.18                        

BUG FIXES

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

                       Changes in version 1.1.16                        

BUG FIXES

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

                       Changes in version 1.1.14                        

SIGNIFICANT USER-VISIBLE CHANGES

  - Completed the change to Gencode v25 annotation for exon and gene
    counts.

                       Changes in version 1.1.13                        

SIGNIFICANT USER-VISIBLE CHANGES

  - We dropped TxDb.Hsapiens.UCSC.hg38.knownGene completely from recount
    and will be using Gencode v25 instead.

                       Changes in version 1.1.12                        

BUG FIXES

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

                        Changes in version 1.1.8                        

SIGNIFICANT USER-VISIBLE CHANGES

  - 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 1.1.6                        

SIGNIFICANT USER-VISIBLE CHANGES

  - snaptron_query() can now access GTEx and TCGA data.

                        Changes in version 1.1.5                        

SIGNIFICANT USER-VISIBLE CHANGES

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

                        Changes in version 1.1.2                        

SIGNIFICANT USER-VISIBLE CHANGES

  - The function reproduce_ranges() now has the db argument. By default
    it's set to TxDb.Hsapiens.UCSC.hg38.knownGene to reproduce the
    actual information used in recount. But it can also be used with
    EnsDb.Hsapiens.v79 to use the ENSEMBL annotation. Then with
    coverage_matrix() you can get the counts for either an updated
    TxDb.Hsapiens.UCSC.hg38.knownGene or for EnsDb.Hsapiens.v79 at the
    exon and/or gene levels as shown in the vignette.

                        Changes in version 1.1.1                        

SIGNIFICANT USER-VISIBLE CHANGES

  - The vignette now describes how to download all the data, how to
    check exon-exon junctions by class, and how to use SciServer compute
    to access all the recount data (over 6 TB) via
    http://www.sciserver.org/

                       Changes in version 0.99.30                       

NEW FEATURES

  - 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

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

                       Changes in version 0.99.0                        

NEW FEATURES

  - Created the package skeleton for recount
  - Added the function reproduce_ranges() for re-creating the gene or
    exon level information used in the recount project.
  - Added the function abstract_search() for identifying SRA projects of
    interest by searching the abstracts.
  - Added the function browse_study() for opening a browser tab for
    further exploring a project.
  - Added the function download_study() for downloading the data from
    the recount project.
  - 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.
  - Added the function expressed_regions() for defining the expressed
    regions in a chromosome for a given SRA study.
  - Added the function coverage_matrix() for computing the coverage
    matrix based on the regions of interest for a given SRA study.
  - Added the function geo_info() for obtaining sample information from
    GEO.
  - 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.
  - Added the function geo_characteristics() for building a data.frame()
    from geo_info()'s results for the characteristics.
  - 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.