Changes in Version 1.9.4 (2024-03-07) ===================================== * Re-added corncob (due to its previous removal from CRAN) * Bug-fix: correct DA_Seurat() due to changes of Seurat::FindMarkers() * Computed DA direction for ANCOM method Changes in Version 1.8.1 (2023-11-04) ===================================== * Porting the changes of devel version 1.9.1 to release Changes in Version 1.9.1 (2023-11-04) ===================================== * Temporarily removed corncob (due to its removal from CRAN) Changes in Version 1.9.0 (2023-10-24) ===================================== * Bump x.y.z version to odd y following creation of RELEASE_3_18 branch Changes in Version 1.8.0 (2023-10-24) ===================================== * Published in Bioconductor release 3.18 Changes in Version 1.7.5 (2023-10-13) ===================================== * Updated DA_Seurat() for the new version * Waiting for bug-fix: DA_ANCOM() (random effects not working) * Waiting for bug-fix: DA_mixMC() (multilevel analysis not working) * Bug-fix: correct dataset name in unit tests * Bug-fix: in DA_ALDEx2() replaced unlist() with as.vector() * Minor documentation updates related to dependencies Changes in Version 1.6.4 (2023-07-22) ===================================== * Porting the changes of devel version 1.7.4 to release Changes in Version 1.7.4 (2023-07-22) ===================================== * Reducing the number of comparisons in vignette to reduce build time Changes in Version 1.6.3 (2023-07-11) ===================================== * Porting the changes of devel version 1.7.3 to release Changes in Version 1.7.3 (2023-07-11) ===================================== * Bug-fix: Minor changes in vignette Changes in Version 1.6.2 (2023-07-09) ===================================== * Porting the changes of devel version 1.7.2 to release Changes in Version 1.7.2 (2023-07-09) ===================================== * Bug-fix for DA_Maaslin2() function Changes in Version 1.6.1 (2023-07-08) ===================================== * Porting the changes of devel version 1.7.1 to release Changes in Version 1.7.1 (2023-07-07) ===================================== * New methods: linDA, Maaslin2, ZicoSeq * New method: mixMC (temporarily unavailable) * Add 'alpha' parameter in DA_ANCOM() Changes in Version 1.7.0 (2023-04-25) ===================================== * Bump x.y.z version to odd y following creation of RELEASE_3_17 branch Changes in Version 1.6.0 (2023-04-25) ===================================== * Published in Bioconductor release 3.17 Changes in Version 1.5.3 (2023-04-20) ===================================== * Add CITATION file * Update README.md file * Add ORCID for authors * Bug-fix for DA_MAST() function Changes in Version 1.5.2 (2022-11-21) ===================================== * Correct FDR description in vignette * Add BiocParallel support for runMocks() and runSplits() functions * Add example for ANCOMBC based methods in parallel Changes in Version 1.5.1 (2022-11-14) ===================================== * Add FDR computation in Type I Error Control analysis * Add BiocParallel support for runMocks() and runSplits() functions * Update vignette Changes in Version 1.5.0 (2022-11-01) ===================================== * New devel version Changes in Version 1.4.0 (2022-11-01) ===================================== * New release version 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