Changelog

Source: NEWS.md

MicrobiomeAnalysis v1.0.3

  • Update codes for selecting taxa level in run_ANOSIM. (2022-11-30)
  • Update codes for selecting taxa level in run_MANTE. (2022-11-30)
  • Update codes for selecting taxa level in run_MRPP. (2022-11-30)
  • Update codes for selecting taxa level and test model in run_PERMANOVA. (2022-11-30)
  • Update codes for selecting taxa level in run_betadisper. (2022-11-30)
  • Update codes for selecting taxa level in run_distance. (2022-11-30)
  • Update codes for selecting taxa level and log formula in transform_abundances. (2022-11-30)
  • Add trim_prevalence. (2022-11-30)
  • Add filter_abundance. (2022-11-30)
  • Add Data Processing in Introduction.Rmd. (2022-11-30)
  • Add .import_dada2_taxa for managing taxa levels. (2022-12-01)
  • Add get_alphaindex for alpha diversity. (2022-12-01)
  • Add impute_abundance for imputing missing values. (2022-12-02)
  • Add scale_variables for scaling variables. (2022-12-02)
  • Add Zeybel_2020 datasets. (2022-12-12)
  • Modify run_ANOSIM, run_betadisper, run_distance, run_MANTEL, run_MRPP and run_PERMANOVA for SummarizedExperiment object. (2022-12-13)
  • Modify impute_abundance, transform_abundances and trim_prevalence for SummarizedExperiment object. (2022-12-14)
  • Modify trim_prevalence for subset SummarizedExperiment object. (2023-1-7)
  • Add import_SE for SummarizedExperiment object. (2023-1-8)
  • Modify scale_variables for SummarizedExperiment object. (2023-1-8)
  • Modify run_lefse for example data. (2023-1-8)
  • Modify filter_abundance for SummarizedExperiment object. (2023-1-10)
  • Modify import_SE for correcting order of samples and features. (2023-1-10)
  • Add run_rarecurve. (2023-1-10)
  • Modify get_alphaindex. (2023-1-10)
  • Modify impute_abundance. (2023-1-12)
  • Remove run_rarecurve. (2023-8-9)
  • Add Alpha diversity and Beta dispersion in Introduction.Rmd. (2023-8-9)
  • Add run_ord and plot_ord. (2023-8-10)
  • Modify process_import_SE, process_imputation, process_transform, and process_trim_prevalence for building SummarizedExperiment object. (2023-8-14)
  • Fix bugs in process_imputation, process_transform, and process_trim_prevalence for building SummarizedExperiment object. (2023-8-16)
  • Fix bugs in plot_ord. (2023-12-1)
  • Add in run_metabolomeDA and plot_volcano. (2023-12-2)
  • Fix bugs in Alldata.R. (2023-12-1)

MicrobiomeAnalysis v1.0.2

MicrobiomeAnalysis v1.0.1

  • Add import_dada2 and import_qiime2. (2022-05-14)
  • Add run_betadisper, run_PERMANOVA, run_MANTEL, run_ANOSIM and run_MRPP. (2022-05-15)