Changes in version 0.99.14                       

SIGNIFICANT USER-VISIBLE CHANGES

  - Added the function enough_ram() which is used to control the
    execution of examples. If it fails when using fetch_data("sce") then
    fetch_data() will show a warning.
  - fetch_data(type = "sce_example") is now supported and used visibly
    in the vignette, eliminating the need for eval = FALSE chunks. This
    should enable testing the vignette code on the Bioconductor Single
    Package Builder on Windows (max 2.5 GB of RAM available).

BUG FIXES

  - Fixed the example in get_colors().
  - Fixed layer_stat_cor_plot() for when min and/or max are specified.

                       Changes in version 0.99.13                       

SIGNIFICANT USER-VISIBLE CHANGES

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

                       Changes in version 0.99.12                       

BUG FIXES

  - Remove the spatialLIBD.Rproj file =( since BioC's SBP is asking me
    to do so
    http://bioconductor.org/spb_reports/spatialLIBD_buildreport_20200303135350.html
  - Use system2() instead of system().
  - Move the set.seed() call outside of layer_boxplot() as noted by
    Martin Morgan
    https://github.com/Bioconductor/Contributions/issues/1389#issuecomment-594099852
    .
  - Use \linkS4class as I see being done at
    https://github.com/drisso/SingleCellExperiment/search?q=linkS4class&unscoped_q=linkS4class.
  - Use vapply() instead of sapply().
  - Fix (or attempt to) some doc links.

                       Changes in version 0.99.11                       

BUG FIXES

  - Check if removing the RcppAnnoy line in the DESCRIPTION actually
    works now based on Aaron Lun's comment at
    https://github.com/eddelbuettel/rcppannoy/issues/57#issuecomment-594097241.

                       Changes in version 0.99.10                       

SIGNIFICANT USER-VISIBLE CHANGES

  - Include AWS links to the image TIFF files (~500mb each) as requested
    by Qian Zhu zqian@jimmy.harvard.edu for visualizing the data on the
    Giotto Viewer https://www.biorxiv.org/content/10.1101/701680v1.

BUG FIXES

  - Fix fetch_data() and the vignette by specifying the mode = "wb" for
    utils::download.file() in order to resolve an issue with Windows OS
    reported here
    http://bioconductor.org/spb_reports/spatialLIBD_buildreport_20200302120158.html#tokay2_buildsrc_anchor.

                       Changes in version 0.99.9                        

SIGNIFICANT USER-VISIBLE CHANGES

  - Link to https://doi.org/10.1101/2020.02.28.969931 now that its
    public.

                       Changes in version 0.99.8                        

SIGNIFICANT USER-VISIBLE CHANGES

  - https://spatial.libd.org/spatialLIBD is not supported since we are
    using Shiny Server and not Shiny Server Pro. So all links have now
    been updated to http://spatial.libd.org/spatialLIBD.

                       Changes in version 0.99.7                        

BUG FIXES

  - Run a test that might help with
    https://github.com/r-lib/pkgdown/issues/1230.

                       Changes in version 0.99.6                        

SIGNIFICANT USER-VISIBLE CHANGES

  - Add mirrors for the shiny app and change the main location.

                       Changes in version 0.99.5                        

SIGNIFICANT USER-VISIBLE CHANGES

  - Make fetch_data() more flexible. Should now work when the data is
    absent.

                       Changes in version 0.99.4                        

BG FIXES

  - Fix Travis badges
  - Fix Kristen's name on the vignette
  - Add the same welcome information to the top of the vignette, since
    this will be what Bioconductor users see first. Basically, we have
    made sure that users will see the same information first regardless
    if they find the package README, open the shiny app, or find the
    package vignette.

                       Changes in version 0.99.3                        

SIGNIFICANT USER-VISIBLE CHANGES

  - Further refine the READMEs (pkg and shiny). They now include the
    list of links to the raw 10x Genomics files as well as a short
    description of the project at the top. This was in response to
    feedback by Andrew Jaffe.

                       Changes in version 0.99.2                        

SIGNIFICANT USER-VISIBLE CHANGES

  - Update main package READMEs to reflect the changes to the shiny web
    app README.md.

                       Changes in version 0.99.1                        

NEW FEATURES

  - Added Kristen R Maynard to the DESCRIPTION file.
  - Improved the shiny app page footer.
  - Moved around the documentation and added a new main tab with an
    overview in response to the feedback by Stephanie Hicks.

                       Changes in version 0.99.0                        

NEW FEATURES

  - Added a NEWS.md file to track changes to the package.
  - First full version of the package to be submitted to Bioconductor.
    Note that the ExperimentHub::ExperimentHub() functionality won't
    work until they approve the package. However, for now fetch_data()
    has a backup mechanism in place.
  - Submitted to Bioconductor here.