Changes in version 1.4.1                        

We report a bug in satuRn 1.4.0. (Bioconductor release 3.15). The bug
was inadvertently introduced in satuRn 1.3.1 (from the former
Bioconductor devel). Note that the bug was not thus present in any of
the older Bioconductor releases 3.13 and 3.14 (satuRn 1.0.x, 1.1.x and
1.2.x).

Bug details:

Imagine a gene with three isoforms and two cell types. The goal is to
assess DTU between cell types. All isoforms are expressed in all cells
of cell type 1. However, none of the isoforms are expressed in any of
the cells in cell type 2 (i.e., the gene is not expressed in cell
type 2).

satuRn computes the log-odds of picking a certain isoform from the pool
of isoforms in each cell type, and then compares these log-odds
estimates between the cell types. However, in this example, the log-odds
of picking a certain isoform from the pool of isoforms in cell type 2
cannot be computed, as there is no data. Hence, the DTU test statistic
should be NA. However, due to erroneous handling of NA estimates, which
was inadvertently introduced in satuRn 1.3.1. while aiming to resolve
github issue 16, the log-odds in cell type 1 will be compared to zero.
Hence, (erroneous) results can be obtained for this contrast, even when
there are no data in cell type 2.

Note that in many cases such isoforms may not pass filtering and would
not get evaluated altogether. However, when analyzing sprase scRNA-Seq
datasets with a lenient filtering criterium, this problem will apply,
and will result in mistakes in the inference.

                        Changes in version 1.4.0                        

satuRn version for Bioconductor release 3.15

                        Changes in version 1.3.1                        

  - Bug fix: allow for fit errors to be propagated as NA results (github
    issue 15 by @jgilis)
  - Bug fix: handle experimental designs with empty factor levels
    correctly (github issue 16 by @XueyiDong)
  - Bug fix: identify transcripts that are the only expressed transcript
    of a gene and set NA results (github issue 17 by @jgilis)
  - Bug fix: handle extreme z-scores in testDTU with diagplot2 option
  - Enhancement: plotDTU now allows for sparseMatrix input

                        Changes in version 1.1.2                        

  - Improved error handling

                        Changes in version 1.1.1                        

  - Initial Bioconductor release of satuRn

                       Changes in version 0.99.0                        

NEW FEATURES

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

SIGNIFICANT USER-VISIBLE CHANGES

  - Your main changes to a function foo() or parameter param.

BUG FIXES

  - Your bug fixes. See more details at
    http://bioconductor.org/developers/package-guidelines/#news.