Changes in Version 1.3.11 (2022-10-31) ===================================== * Updated DA_ANCOM with the new ancombc2 method Changes in Version 1.3.10 (2022-10-20) ===================================== * Re-adapted p-values extraction from DA_ALDEx2() with test = "glm" Changes in Version 1.3.9 (2022-09-18) ===================================== * Re-added corncob after temporary removal in v1.3.5 Changes in Version 1.3.8 (2022-09-18) ===================================== * Bug-fix for table headers in chapter 3 of the vignette Changes in Version 1.3.7 (2022-09-18) ===================================== * Added more informations about the methods in chapter 3 of the vignette Changes in Version 1.2.5 (2022-09-10) ===================================== * Porting the changes of devel version 1.3.6 to release Changes in Version 1.3.6 (2022-09-10) ===================================== * Simplified the vignette Changes in Version 1.2.4 (2022-09-07) ===================================== * Porting the changes of devel version 1.3.5 to release Changes in Version 1.3.5 (2022-09-07) ===================================== * Temporarily removed corncob. New version of detectseparation v0.3 broke it. * Updated intro vignette accordingly. Changes in Version 1.2.3 (2022-09-07) ===================================== * Porting the changes of devel version 1.3.4 to release Changes in Version 1.3.4 (2022-09-07) ===================================== * Updated intro vignette. * Removed HMP16SData chunks. * Added conditional usage of kableExtra * Removed dependency from HMP16SData and ffpe * Implemented CAT function instead of using ffpe::CATplot Changes in Version 1.2.2 (2022-09-06) ===================================== * Porting the changes of devel version 1.3.3 to release Changes in Version 1.3.3 (2022-09-06) ===================================== * In DA_basic changed logFC calculation when paired = TRUE * In intro vignette corrected the number of comparisons from 10 to 2 Changes in Version 1.2.1 (2022-09-03) ===================================== * Porting the changes of devel version 1.3.2 to release Changes in Version 1.3.2 (2022-09-03) ===================================== * Changes after the first revision from the "Bioinformatics" journal * Improved vignette with more descriptions, new methods, and more chapters * Improved warning and error messages * Support for TreeSummarizedExperiment object * New function get_count_metadata() to access counts and metadata of a phyloseq or TreeSummarizedExperiment object. * Added the "fitFeatureModel" implementation in DA_metagenomeSeq() * "CSS" normalization factors are now returned as they are, not divided by a scaling factor * Replaced "CSS_median" and "CSS_default" normalizations with "CSS" * Added the "kw" and "glm" implementation in DA_ALDEx2() * Added the "paired.test" option in DA_ALDEx2() for "t" and "wilcox" tests * Added support for "CLR", "RC", and "none" normalization methods in DA_Seurat() * Added support for "scale.factor" in DA_Seurat() * Added more controls and verbosity regarding normalizations and DA methods * Added the plotLogP() function for plottin the negative log p-values distribution * Added DA_NOISeq(), DA_dearseq(), DA_ANCOM(), and DA_basic() to the pool of methods * added detectseparation (<= 0.2.0) to the "Imports", new version 0.3 not compatible with corncob 0.2 Changes in Version 1.3.1 (2022-05-16) ===================================== * Updated intro vignette * Added more citations and authors * Added figure captions and references Changes in Version 1.3.0 (2022-04-26) ===================================== * Bump x.y.z version to odd y following creation of RELEASE_3_15 branch Changes in Version 1.2.0 (2022-04-26) ===================================== * Published in Bioconductor release 3.15 Changes in Version 1.1.1 (2022-03-21) ===================================== * Corrected a bug in DA_ALDEx2 function * Updated DA_ALDEx2 function manual * Added more authors in the citation Changes in Version 1.1.0 (2021-10-26) ===================================== * Bump x.y.z version to odd y following creation of RELEASE_3_14 branch Changes in Version 1.0.0 (2021-10-26) ===================================== * Published in Bioconductor release 3.14 Changes in Version 0.99.4 (2021-10-15) ===================================== * Changed stats::coef to stats4::coef Changes in Version 0.99.3 (2021-10-15) ===================================== * Added the plotIt = FALSE option for plotRMSE function * Added some more explanations into the "Goodness of Fit" chapter * fitNB, fitZINB, fitHURDLE, fitZIG, and fitDM functions now work with both phyloseq object or count matrices Changes in Version 0.99.2 (2021-10-11) ===================================== * Changed dependency from R 4.0.0 to 4.1.0 * Added example for iterative_ordering() function * Removed the usage of @ to access object's slot in the vignette * Removed a suppressMessages() and a suppressWarnings() from createTIEC() * Added verbosity to createTIEC() function * Added NEWS file Changes in Version 0.99.1 (2021-10-04) ===================================== * Removed unnecessary files Changes in Version 0.99.0 (2021-09-29) ===================================== * Bumped version for submission to Bioconductor * Added README.md file