Changes in version 1.1.9 o Allow selection of number of reads to load from FastQ file in prep and split functions. Default: 1M reads (1e9). o Minor fixes BiocCheck. Changes in version 1.1.8 o Use `query_regions` to select the restriction fragments to use for differential testing in `diffWaldUMI4C`. Changes in version 1.1.7 o Fixed bug with limits of the log2 OR values when plotting differential windows. Changes in version 1.1.6 o Fixed bug in creation of gene annotation when an exon belongs to more than one transcript. o Fixed bug when only one sample is provided (no name in assay columns). Changes in version 1.1.5 o Fixed bug in selection of reference UMI4C sample when more than 1 sample has the same number of total UMIs. Now it will select the first one. The selection of sample to use as reference can be overriden by the `ref_umi4c` argument. Changes in version 1.1.4 o Fixed bug in domainogram plotting where white color was not aligned with 0 log2 FC. Changes in version 1.1.3 o Fixed bug when providing a reference sample to use for normalizing UMI counts. Changes in version 1.1.2 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 o 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. UPDATES 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.