NEWS

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benchdamic 1.13.1 (2024-11-20)

• Bug-fix: changed an internal parameter of DA_ANCOM() to make it works after the new release

benchdamic 1.13.0 (2024-10-29)

• Bump x.y.z version to odd y following creation of RELEASE_3_20 branch

benchdamic 1.12.1 (2024-11-20)

• Porting the changes of devel version 1.13.1 to release

benchdamic 1.12.0 (2024-10-29)

• Published in Bioconductor release 3.20

benchdamic 1.11.1 (2024-09-23)

• Bug-fix: getDA() function now correctly orders results
• Modify Maaslin2 feature names to match the original names

benchdamic 1.11.0 (2024-04-30)

• Bump x.y.z version to odd y following creation of RELEASE_3_19 branch

benchdamic 1.10.1 (2024-09-23)

• Porting the changes of devel version 1.11.1 to release

benchdamic 1.10.0 (2024-04-30)

• Published in Bioconductor release 3.19

benchdamic 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

benchdamic 1.9.1 (2023-11-04)

• Temporarily removed corncob (due to its removal from CRAN)

benchdamic 1.9.0 (2023-10-24)

• Bump x.y.z version to odd y following creation of RELEASE_3_18 branch

benchdamic 1.8.1 (2023-11-04)

• Porting the changes of devel version 1.9.1 to release

benchdamic 1.8.0 (2023-10-24)

• Published in Bioconductor release 3.18

benchdamic 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

benchdamic 1.7.4 (2023-07-22)

• Reducing the number of comparisons in vignette to reduce build time

benchdamic 1.7.3 (2023-07-11)

• Bug-fix: Minor changes in vignette

benchdamic 1.7.2 (2023-07-09)

• Bug-fix for DA_Maaslin2() function

benchdamic 1.7.1 (2023-07-07)

• New methods: linDA, Maaslin2, ZicoSeq
• New method: mixMC (temporarily unavailable)
• Add 'alpha' parameter in DA_ANCOM()

benchdamic 1.7.0 (2023-04-25)

• Bump x.y.z version to odd y following creation of RELEASE_3_17 branch

benchdamic 1.6.4 (2023-07-22)

• Porting the changes of devel version 1.7.4 to release

benchdamic 1.6.3 (2023-07-11)

• Porting the changes of devel version 1.7.3 to release

benchdamic 1.6.2 (2023-07-09)

• Porting the changes of devel version 1.7.2 to release

benchdamic 1.6.1 (2023-07-08)

• Porting the changes of devel version 1.7.1 to release

benchdamic 1.6.0 (2023-04-25)

• Published in Bioconductor release 3.17

benchdamic 1.5.3 (2023-04-20)

• Add CITATION file
• Update README.md file
• Add ORCID for authors
• Bug-fix for DA_MAST() function

benchdamic 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

benchdamic 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

benchdamic 1.5.0 (2022-11-01)

• New devel version

benchdamic 1.4.0 (2022-11-01)

• New release version

benchdamic 1.3.11 (2022-10-31)

• Updated DA_ANCOM with the new ancombc2 method

benchdamic 1.3.10 (2022-10-20)

• Re-adapted p-values extraction from DA_ALDEx2() with test = "glm"

benchdamic 1.3.9 (2022-09-18)

• Re-added corncob after temporary removal in v1.3.5

benchdamic 1.3.8 (2022-09-18)

• Bug-fix for table headers in chapter 3 of the vignette

benchdamic 1.3.7 (2022-09-18)

• Added more informations about the methods in chapter 3 of the vignette

benchdamic 1.3.6 (2022-09-10)

• Simplified the vignette

benchdamic 1.3.5 (2022-09-07)

• Temporarily removed corncob. New version of detectseparation v0.3 broke it.
• Updated intro vignette accordingly.

benchdamic 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

benchdamic 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

benchdamic 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

benchdamic 1.3.1 (2022-05-16)

• Updated intro vignette
• Added more citations and authors
• Added figure captions and references

benchdamic 1.3.0 (2022-04-26)

• Bump x.y.z version to odd y following creation of RELEASE_3_15 branch

benchdamic 1.2.5 (2022-09-10)

• Porting the changes of devel version 1.3.6 to release

benchdamic 1.2.4 (2022-09-07)

• Porting the changes of devel version 1.3.5 to release

benchdamic 1.2.3 (2022-09-07)

• Porting the changes of devel version 1.3.4 to release

benchdamic 1.2.2 (2022-09-06)

• Porting the changes of devel version 1.3.3 to release

benchdamic 1.2.1 (2022-09-03)

• Porting the changes of devel version 1.3.2 to release

benchdamic 1.2.0 (2022-04-26)

• Published in Bioconductor release 3.15

benchdamic 1.1.1 (2022-03-21)

• Corrected a bug in DA_ALDEx2 function
• Updated DA_ALDEx2 function manual
• Added more authors in the citation

benchdamic 1.1.0 (2021-10-26)

• Bump x.y.z version to odd y following creation of RELEASE_3_14 branch

benchdamic 1.0.0 (2021-10-26)

• Published in Bioconductor release 3.14

benchdamic 0.99.4 (2021-10-15)

• Changed stats::coef to stats4::coef

benchdamic 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

benchdamic 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

benchdamic 0.99.1 (2021-10-04)

• Removed unnecessary files

benchdamic 0.99.0 (2021-09-29)

• Bumped version for submission to Bioconductor
• Added README.md file