Changelog

Source: NEWS.md

CHANGES IN VERSION 1.13.7 (2025-08-02):

• fixing a bug with DESeq2::DESeqDataSet input checks

CHANGES IN VERSION 1.13.6 (2025-03-06):

• added C++ code to speed-up computational bottlenecks in permutation tests creating a new dependence on RcppEigen
• added a pkgdown companion website at https://borishejblum.github.io/dearseq/
• fixing vignette last plot

CHANGES IN VERSION 1.13.4 (2023-09-06):

• better handling of non-tested genes

CHANGES IN VERSION 1.13.3 (2023-06-16):

• bug fix on Linux: default number of cores for parallel computations is now detect_cores(logical=FALSE) - 1

CHANGES IN VERSION 1.12.1 (2023-05-28):

• weights_var2test_condi is enforced to FALSE for the permutation test

CHANGES IN VERSION 1.11.1 (2023-03-16):

• add parallel support on Windows

CHANGES IN VERSION 1.9.4 (2022-07-20):

• use scattermore:: in plot_weights()

CHANGES IN VERSION 1.8.3 (2022-07-13):

• fixed a bug in NA handling with which_weights != “none”

CHANGES IN VERSION 1.8.1 (2022-04-28):

• fixed a small bug in permutation p-values introduced with the 1.8.0 release

CHANGES IN VERSION 1.7.2 (2022-04-13):

• reintroduced CompQuadForm::davies() as a longer alternative when the "saddlepoint" method in survey::pchisqsum() fails for computing quadratic form asymptotic p-values

CHANGES IN VERSION 1.7.1 (2022-02-07):

• added a spaghetti plot functionality

CHANGES IN VERSION 1.5.1 (2021-09-01):

• switching from CompQuadForm::davies() to the "saddlepoint" method from survey::pchisqsum() for computing quadratic form asymptotic p-values

CHANGES IN VERSION 1.3.0 (2021-03-09):

• adding plotting capabilities

CHANGES IN VERSION 1.2.0 (2020-05-20):

• adding adaptive permutations

INITIAL RELEASE - VERSION 1.0.0 (2019-11-26):

• this is a reboot of the tcgsaseq package