NEWS

---

UMI4Cats 1.1.9

• Allow selection of number of reads to load from FastQ file in prep and split functions. Default: 1M reads (1e9).
• Minor fixes BiocCheck.

UMI4Cats 1.1.8

• Use 'query_regions' to select the restriction fragments to use for differential testing in 'diffWaldUMI4C'.

UMI4Cats 1.1.7

• Fixed bug with limits of the log2 OR values when plotting differential windows.

UMI4Cats 1.1.6

• Fixed bug in creation of gene annotation when an exon belongs to more than one transcript.
• Fixed bug when only one sample is provided (no name in assay columns).

UMI4Cats 1.1.5

• 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.

UMI4Cats 1.1.4

• Fixed bug in domainogram plotting where white color was not aligned with 0 log2 FC.

UMI4Cats 1.1.3

• Fixed bug when providing a reference sample to use for normalizing UMI counts.

UMI4Cats 1.1.2

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

UMI4Cats 0.99.21

• Improvements in vignette and documentation.

UMI4Cats 0.99.20

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

UMI4Cats 0.99.19

• Minor documentation changes to pass Bioconductor checks.

UMI4Cats 0.99.18

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

UMI4Cats 0.99.17

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

UMI4Cats 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.

UPDATES

• 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()'.
• Added new statistical test using DESeq2: 'differentialNbinomWaldTestUMI4C()'.

UMI4Cats 0.99.15

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

UMI4Cats 0.99.14

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

UMI4Cats 0.99.11

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

UMI4Cats 0.99.10

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

UMI4Cats 0.99.9

• Add data object 'ex_ciita_umi4c' to use in examples and reduce check running times.

UMI4Cats 0.99.8

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

UMI4Cats 0.99.7

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

UMI4Cats 0.99.6

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

UMI4Cats 0.99.5

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

UMI4Cats 0.99.4

• Added '.Rproj' files to .gitignore

UMI4Cats 0.99.3

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

UMI4Cats 0.99.2

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

UMI4Cats 0.99.1

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

UMI4Cats 0.99.0

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