NEWS

Changes in version 1.5.17 (2021-04-22):
+ Continued working on associationTest, now allowing the extra contrasts implemented in the point below (version 1.5.02), to also be used in the case of multiple conditions. This caused some issues with inverting the variance-covariance matrix of the contrasts, which has led to the introduction of a new argument 'inverse', which specifies the procedure to invert this variance-covariance matrix.

Changes in version 1.5.02 (2021-01-21):
+ Major update on associationTest, where the contrasts no longer rely on the knots but rather rely on a new nPoints argument, that specifies the number of points to use per lineage in the contrast. The associationTest also has a new argument contrastType that allows to use three different contrast types to do the test. See the docs on associationTest for more details. Note that results can change significantly depending on the type of contrast chosen, especially in combination with a fold-change cut-off (the l2fc argument).

Changes in version 1.3.19 (2020-10-16):
+ Merged `conditions` branch into `master`. Now the `master` branch can therefore handle multiple conditions. There is a new `conditions` argument in `fitGAM` to handle that, and a condition-specific smoother will be fitted for each lineage. There is also a new test, `conditionTest`, which tests for DE between conditions within a lineage. The way this is done under the hood is exactly like the `patternTest`.

Changes in version 1.1.07 (2020-02-27):
+ added testing against fold change cut-off for all DE tests
+ default cut-off for deciding the rank of the variance-covariance matrix changed in patternTest and earlyDETest. This can impact the results of these tests. To return to original behaviour, set `eigenThresh=1e-8` argument.

Changes in version 0.99.9902 (2019-10-23)
+ tradeSeq's fitGam and evaluateK functions do not have a seed argument anymore, as per Bioconductor's guidelines. Users are encouraged to set the seed manually with the set.seed function before running those functions for reproducibility purposes.

Changes in version 0.99.47 (2019-09-02)
+ tradeSeq now provides `singleCellExperiment` output
  o fitGam now accepts a `slingshotDataSet` object as input
  o All tests and plotting functions accept a `singleCellExperiment` object that contain tradeSeq output

Changes in version 0.99.0 (2019-06-22)
+ Submitted to Bioconductor

Changes in version 0.9.0 (2019-03-15)
+ Reformatted to fulfill Bioconductor guidelines