Changes in version 1.15.3 (2025-07-29) o Minor changes related to warn_prevalence and small_random_effects parameters in DA_maaslin3 Changes in version 1.15.2 (2025-04-24) o Bug-fix: add 'microbiome' among Imports due to an error in some systems Changes in version 1.15.1 (2025-04-22) o New method: maaslin3 o Re-added mixMC Changes in version 1.15.0 (2025-04-15) o Bump x.y.z version to odd y following creation of RELEASE_3_21 branch Changes in version 1.14.3 (2025-07-29) o Porting the changes of devel version 1.15.3 to release Changes in version 1.14.2 (2025-04-24) o Porting the changes of devel version 1.15.2 to release Changes in version 1.14.1 (2025-04-22) o Porting the changes of devel version 1.15.1 to release Changes in version 1.14.0 (2025-04-15) o Published in Bioconductor release 3.21 Changes in version 1.13.1 (2024-11-20) o Bug-fix: changed an internal parameter of DA_ANCOM() to make it works after the new release Changes in version 1.13.0 (2024-10-29) o Bump x.y.z version to odd y following creation of RELEASE_3_20 branch Changes in version 1.12.1 (2024-11-20) o Porting the changes of devel version 1.13.1 to release Changes in version 1.12.0 (2024-10-29) o Published in Bioconductor release 3.20 Changes in version 1.11.1 (2024-09-23) o Bug-fix: getDA() function now correctly orders results o Modify Maaslin2 feature names to match the original names Changes in version 1.11.0 (2024-04-30) o Bump x.y.z version to odd y following creation of RELEASE_3_19 branch Changes in version 1.10.1 (2024-09-23) o Porting the changes of devel version 1.11.1 to release Changes in version 1.10.0 (2024-04-30) o Published in Bioconductor release 3.19 Changes in version 1.9.4 (2024-03-07) o Re-added corncob (due to its previous removal from CRAN) o Bug-fix: correct DA_Seurat() due to changes of Seurat::FindMarkers() o Computed DA direction for ANCOM method Changes in version 1.9.1 (2023-11-04) o Temporarily removed corncob (due to its removal from CRAN) Changes in version 1.9.0 (2023-10-24) o Bump x.y.z version to odd y following creation of RELEASE_3_18 branch Changes in version 1.8.1 (2023-11-04) o Porting the changes of devel version 1.9.1 to release Changes in version 1.8.0 (2023-10-24) o Published in Bioconductor release 3.18 Changes in version 1.7.5 (2023-10-13) o Updated DA_Seurat() for the new version o Waiting for bug-fix: DA_ANCOM() (random effects not working) o Waiting for bug-fix: DA_mixMC() (multilevel analysis not working) o Bug-fix: correct dataset name in unit tests o Bug-fix: in DA_ALDEx2() replaced unlist() with as.vector() o Minor documentation updates related to dependencies Changes in version 1.7.4 (2023-07-22) o Reducing the number of comparisons in vignette to reduce build time Changes in version 1.7.3 (2023-07-11) o Bug-fix: Minor changes in vignette Changes in version 1.7.2 (2023-07-09) o Bug-fix for DA_Maaslin2() function Changes in version 1.7.1 (2023-07-07) o New methods: linDA, Maaslin2, ZicoSeq o New method: mixMC (temporarily unavailable) o Add 'alpha' parameter in DA_ANCOM() Changes in version 1.7.0 (2023-04-25) o Bump x.y.z version to odd y following creation of RELEASE_3_17 branch Changes in version 1.6.4 (2023-07-22) o Porting the changes of devel version 1.7.4 to release Changes in version 1.6.3 (2023-07-11) o Porting the changes of devel version 1.7.3 to release Changes in version 1.6.2 (2023-07-09) o Porting the changes of devel version 1.7.2 to release Changes in version 1.6.1 (2023-07-08) o Porting the changes of devel version 1.7.1 to release Changes in version 1.6.0 (2023-04-25) o Published in Bioconductor release 3.17 Changes in version 1.5.3 (2023-04-20) o Add CITATION file o Update README.md file o Add ORCID for authors o Bug-fix for DA_MAST() function Changes in version 1.5.2 (2022-11-21) o Correct FDR description in vignette o Add BiocParallel support for runMocks() and runSplits() functions o Add example for ANCOMBC based methods in parallel Changes in version 1.5.1 (2022-11-14) o Add FDR computation in Type I Error Control analysis o Add BiocParallel support for runMocks() and runSplits() functions o Update vignette Changes in version 1.5.0 (2022-11-01) o New devel version Changes in version 1.4.0 (2022-11-01) o New release version Changes in version 1.3.11 (2022-10-31) o Updated DA_ANCOM with the new ancombc2 method Changes in version 1.3.10 (2022-10-20) o Re-adapted p-values extraction from DA_ALDEx2() with test = "glm" Changes in version 1.3.9 (2022-09-18) o Re-added corncob after temporary removal in v1.3.5 Changes in version 1.3.8 (2022-09-18) o Bug-fix for table headers in chapter 3 of the vignette Changes in version 1.3.7 (2022-09-18) o Added more informations about the methods in chapter 3 of the vignette Changes in version 1.3.6 (2022-09-10) o Simplified the vignette Changes in version 1.3.5 (2022-09-07) o Temporarily removed corncob. New version of detectseparation v0.3 broke it. o Updated intro vignette accordingly. Changes in version 1.3.4 (2022-09-07) o Updated intro vignette. o Removed HMP16SData chunks. o Added conditional usage of kableExtra o Removed dependency from HMP16SData and ffpe o Implemented CAT function instead of using ffpe::CATplot Changes in version 1.3.3 (2022-09-06) o In DA_basic changed logFC calculation when paired = TRUE o In intro vignette corrected the number of comparisons from 10 to 2 Changes in version 1.3.2 (2022-09-03) o Changes after the first revision from the "Bioinformatics" journal o Improved vignette with more descriptions, new methods, and more chapters o Improved warning and error messages o Support for TreeSummarizedExperiment object o New function get_count_metadata() to access counts and metadata of a phyloseq or TreeSummarizedExperiment object. o Added the "fitFeatureModel" implementation in DA_metagenomeSeq() o "CSS" normalization factors are now returned as they are, not divided by a scaling factor o Replaced "CSS_median" and "CSS_default" normalizations with "CSS" o Added the "kw" and "glm" implementation in DA_ALDEx2() o Added the "paired.test" option in DA_ALDEx2() for "t" and "wilcox" tests o Added support for "CLR", "RC", and "none" normalization methods in DA_Seurat() o Added support for "scale.factor" in DA_Seurat() o Added more controls and verbosity regarding normalizations and DA methods o Added the plotLogP() function for plottin the negative log p-values distribution o Added DA_NOISeq(), DA_dearseq(), DA_ANCOM(), and DA_basic() to the pool of methods o 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) o Updated intro vignette o Added more citations and authors o Added figure captions and references Changes in version 1.3.0 (2022-04-26) o Bump x.y.z version to odd y following creation of RELEASE_3_15 branch Changes in version 1.2.5 (2022-09-10) o Porting the changes of devel version 1.3.6 to release Changes in version 1.2.4 (2022-09-07) o Porting the changes of devel version 1.3.5 to release Changes in version 1.2.3 (2022-09-07) o Porting the changes of devel version 1.3.4 to release Changes in version 1.2.2 (2022-09-06) o Porting the changes of devel version 1.3.3 to release Changes in version 1.2.1 (2022-09-03) o Porting the changes of devel version 1.3.2 to release Changes in version 1.2.0 (2022-04-26) o Published in Bioconductor release 3.15 Changes in version 1.1.1 (2022-03-21) o Corrected a bug in DA_ALDEx2 function o Updated DA_ALDEx2 function manual o Added more authors in the citation Changes in version 1.1.0 (2021-10-26) o Bump x.y.z version to odd y following creation of RELEASE_3_14 branch Changes in version 1.0.0 (2021-10-26) o Published in Bioconductor release 3.14 Changes in version 0.99.4 (2021-10-15) o Changed stats::coef to stats4::coef Changes in version 0.99.3 (2021-10-15) o Added the plotIt = FALSE option for plotRMSE function o Added some more explanations into the "Goodness of Fit" chapter o 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) o Changed dependency from R 4.0.0 to 4.1.0 o Added example for iterative_ordering() function o Removed the usage of @ to access object's slot in the vignette o Removed a suppressMessages() and a suppressWarnings() from createTIEC() o Added verbosity to createTIEC() function o Added NEWS file Changes in version 0.99.1 (2021-10-04) o Removed unnecessary files Changes in version 0.99.0 (2021-09-29) o Bumped version for submission to Bioconductor o Added README.md file