NEWS.md

In HuaZou/MicrobiomeAnalysis: Data analysis toolkits in metagenomics

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)
• Modify run_ord and plot_ord for SummarizedExperiment-class object. (2024-2-22)
• Fix bugs in run_ancombc for replacing zero_cut by prv_cut using ANCOMBC::ancombc (v2.4.0). (2024-2-22)

MicrobiomeAnalysis v1.0.2

• Add differential analysis scripts from microbiomeMarker. (2022-05-18)

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)

Initial repository(2022-05-14)

• Submitted to github.

HuaZou/MicrobiomeAnalysis documentation built on May 13, 2024, 11:10 a.m.