v1.0.3

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)

v1.0.1

MicrobiomeAnalysis v1.0.1

Convert inputs into phyloseq-class object

1. inputs from dada2
2. inputs from qiime2

Multivariate Community Analysis

1. Multivariate homogeneity of groups dispersions (variances)
2. Permutational Multivariate Analysis of Variance (PERMANOVA)
3. Mantel Test (MANTEL)
4. Analysis of Similarity (ANOSIM)
5. Multi-response Permutation Procedures (MRPP)