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

  o Fixed bug when `cut_pos`!=0 that generated a gap in the digested genome
    object (see issue #8)

CHANGES IN VERSION 0.99.21
--------------------------

  o Improvements in vignette and documentation.

CHANGES IN VERSION 0.99.20
--------------------------

  o Avoid duplication of fragment end calculation in plotDifferential for 
    DESeq2 results.

CHANGES IN VERSION 0.99.19
--------------------------

  o Minor documentation changes to pass Bioconductor checks.


CHANGES IN VERSION 0.99.18
--------------------------

  o Fix DESeq2 example.
  o Reduce size of installed example tsv.gz count files.
  

CHANGES IN VERSION 0.99.17
--------------------------

  o Re-run example datasets and use again links from figshare.

CHANGES IN VERSION 0.99.16
--------------------------

! Important: This version is not compatible with the .tsv.gz files created by
previous versions. You will need to run `contactsUMI4C()` again to generate
updated .tsv.gz files.

  o Improved grouping arguments for UMI-4C objects: now creates a new UMI-4C
    object that can be accessed using `groupsUMI4C(umi4c)$condition`. This allows
    retaining replicate information in the main UMI4C object while allowing 
    plotting grouped trends stored in `groupsUMI4C()`.
    
  o Added new statistical test using DESeq2: `differentialNbinomWaldTestUMI4C()`. 

CHANGES IN VERSION 0.99.15
--------------------------

  o Fixed duplicated read number in read id (.singlePrepUMI4C) (see issue #5).
  o Changed example download urls to gattaca server.

CHANGES IN VERSION 0.99.14
--------------------------

  o Fixed bug where adaptive smoothed trend was normalized twice (see issue #4).

CHANGES IN VERSION 0.99.11
--------------------------

  o Uploaded example datasets urls in `downloadUMI4CexampleData()` to a more
    stable and permanent location (figshare.com).

CHANGES IN VERSION 0.99.10
--------------------------

  o Avoid running long and redundant examples, already tested in the vignette to
    avoid TIMEOUT build error.

CHANGES IN VERSION 0.99.9
--------------------------

  o Add data object `ex_ciita_umi4c` to use in examples and reduce check running
    times.

CHANGES IN VERSION 0.99.8
--------------------------

  o Update package vignette to clarify the origin of the different sample files
    used to exemplify a workflow using the UMI4Cats package.

CHANGES IN VERSION 0.99.7
--------------------------

  o Added unit tests using `testthat`.
  o Use BiocFileCache to download sample files.
  o Use tempdir() for demo purposes both in vignette and examples.
  o Added inst\scripts to describe how the sample data was generated.
  o Other minor changes to comply with Bioconductor review
    (see https://github.com/Pasquali-lab/UMI4Cats/issues/2#issue-637249954)

CHANGES IN VERSION 0.99.6
--------------------------

  o Delete downloaded and intermediate folders when building vignette.
  o Added `UMI4Cats_index` to .Rbuildignore to prevent ERRORs and
    WARNINGs in BioCCheck.

CHANGES IN VERSION 0.99.5
--------------------------

  o Increased speed of `getViewpointCoordinates()` by allowing pre-selection
    of viewpoint chromosome using `sel_seqname` argument.
  o Added reduced fastq files in extdata and allow downloading of reduced
    bowtie index to increase vignette building speed.

CHANGES IN VERSION 0.99.4
--------------------------

  o Added `.Rproj` files to .gitignore

CHANGES IN VERSION 0.99.3
--------------------------

  o Changed example in vignette and manuals to *CIITA*.
  o Added viewpoint name in `plotTrend()`.
  o Improved multi-panel plotting of `plotUMI4C()`.

CHANGES IN VERSION 0.99.2
--------------------------

  o Allow `ref_umi4c` to be used as reference for plotting colors, domainogram
    and differential analysis (not only for normalization).
  o Fixed error when using `sampleID` as `grouping` variable in `makeUMI4C()`.
  o Fixed bug in `results()` when `fomat=data.frame` and `ordered=TRUE`.
  o Improved visualization of differential regions reconverting `Inf` and `-Inf`
    to maximum and minimum (respectively) odd's ratio values.
  o Add more functionality details in the `Analyzing UMI-4C data with UMI4Cats`
    vignette.

CHANGES IN VERSION 0.99.1
--------------------------

  o Fixed error in function `createGeneAnnotation` and `plotGenes` that occurs
    when there are no genes in the region or a gene has multiple identifiers.
  o  Fixed duplicated generics definition for `SummarizedExperiment` objects to
    avoid error when reloading the package.
  o Fixed error when `bait_exclusion` is set to 0.
  o Added possibility to specify the sample to use as reference for normalization
    (`ref_umi4c` argument in `makeUMI4C`).
  o Now the `grouping` variable in `makeUMI4C()` is used more upstream in the
    analysis. For using different grouping variables, user must create different
    `UMI4C` objects.
  o Fixed bug where sometimes bait coordinates in the output tsv file are `NA`.
  o `statsUMI4C` now also outputs a stats summary table in `wk_dir/logs/stats_summary.txt`.
  o Improve function documentation.
  o Improve pkgdown UMI4Cats site.
  o Rewrite and improve the `Analyzing UMI-4C data with UMI4Cats` vignette.

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

  o First public release of UMI4Cats.
  o Added a `NEWS.md` file to track changes to the package.
