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XbiomeAnalysis / XMAS_tutorial

XMAS 2.0 tutorial

Home Page:https://xbiomeanalysis.github.io/XMAS_tutorial

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XMAS2 Tutorial

đź“– Chapters

This tutorial was organized according to the XMAS 2.0 functions.

  • In the beginning two chapters, we specially provided the basic requirements of bioinformatics and overview on microbiota, and the installation of XMAS.

  • In Chapter 3, we convert the results from in-house pipeline into phyloseq-class object for downstream data analysis.

  • In Chapter 4 provided the functions to evaluate the data quality.

  • In Chapter 5, we introduced the preprocessing methods on microbiota data before differential analysis.

  • In Chapter 6 provided the alpha diversity analysis.

  • In Chapter 7 provided the beta diversity analysis.

  • In Chapter 8 provided the microbiota composition analysis.

  • In Chapter 9 provided the core microbiota analysis.

  • In Chapter 10 provided the differential analysis.

  • In Chapter 11 provided some functions for visualization.

  • In Chapter 12 provided the association analysis.

  • In Chapter 13 showed the principals of the differential analysis methods.

  • In Chapter 14 provided the examples by using XMAS 2.0 on microbiota data.

✍️ Authors

  1. Hua Zou

🔧 Change log

XMAS 2.2.0

XMAS 2.1.9

  • fix bugs sideboxplot order in plot_Ordination. (2023-5-11)
  • fix bugs in plot_volcano for wrong typing of Nonsignif. (2023-5-17)
  • add lib_cutoff parameter in run_ancom for controlling threshold of library size. (2023-5-17)
  • fix bugs in plot_volcano for unmatched legend colors showed the number of significant features. (2023-5-17)
  • add codes in plot_barplot, plot_boxplot, and plot_dotplot for adding more spaces on y axis. (2023-5-18)
  • fix bugs in run_RefCheck for correcting the parameter of output directory. (2023-5-23)
  • add TaxaNumber alpha index in run_alpha_diversity. (2023-5-25)
  • fix bugs in plot_metaphlanTrack and plot_Ordination for ordering multiple groups in legend. (2023-5-26)
  • add the procedures on generation of merged metphlan table in get_metaphlan_phyloseq. (2023-5-26)
  • fix bugs in run_alpha_diversity for measures only with "Evenness" and "TaxaNumber". (2023-6-6)
  • add order list of subgroup in plot_StackBarPlot for sorting elements of subgroup. (2023-6-15)
  • update list of spike-in species in run_RefCheck. (2023-6-19)
  • update list of spike-in species in aggregate_LOD_taxa. (2023-6-19)
  • update spike-in species list of BRS Reference Matrix in metaphlan2 and metaphlan3. (2023-6-21)
  • fix bugs in plot_StackBarPlot for orderSample. (2023-7-25)
  • fix bugs in check_sample_names for taxa table (2023-8-3)
  • add plot_ContrTaxa for display the contributed taxa in the specific metacyc pathway (2023-8-11)
  • add run_filter3 according to Lee et al (2022 Nature medicine). (2023-8-22)
  • fix bugs in run_filter for mean relative abundance (2023-8-22)
  • update list of spike-in species by removing s__Eggerthella_lenta in run_RefCheck. (2023-9-13)
  • fix bugs in preprocess_ps for transpose otu table (2023-9-13)
  • update BRS Reference Matrix in metaphlan2 and metaphlan3 in extdata folder. (2023-9-13)
  • fix bugs in run_ordination and plot_Ordination for NA values in group. (2023-9-15)
  • update BRS Reference Matrix for 8 gold BRS. (2023-9-21)
  • create run_RefCheck2 for impurity criterion in 16s. (2023-9-21)
  • add deprecated functions (deprecate run_RefCheck and run_lefse) (2023-9-21)
  • fix bugs in run_multiple_da for modifying parameters. (2023-9-21)
  • update calculation of bray distance for 8 16s gold BRS by splitting into two vendors. (2023-9-28)
  • add run_Mul_RefCheck for quality control of multiple BRS. (2023-10-9)
  • modify norm parameters in run_wilcox. (2023-10-26)
  • modify norm parameters in run_ttest. (2023-10-26)

XMAS 2.1.8

  • update scripts of differential analysis with alias of taxa names. (2022-09-13)
  • modify preprocess_ps. (2022-09-13)
  • add plot_metaphlanTrack. (2022-09-15)
  • add run_beta_dispersion. (2022-09-29)
  • update plot_metaphlanTrack. (2022-10-08)
  • update import_metaphlan_taxa for selecting k__Bacteria. (2022-10-17)
  • update aggregate_LOD_taxa for remaining BRS species. (2022-10-28)
  • update aggregate_LOD_taxa for correcting relative abundance. (2022-11-07)
  • update run_RefCheck with new BRS species. (2022-11-07)
  • update run_wilcox and run_ttest with default normalization method (CLR). (2022-11-08)
  • update BRS Species_ref.csv with 27 species. (2022-11-09)
  • fix bugs (wrong return values) in aggregate_LOD_taxa. (2022-11-09)
  • update summarize_taxa for meeting one sample. (2022-11-09)
  • fix bugs (wrong order on sample data) preprocess_ps. (2022-11-15)
  • modify and add new parameters in import_metaphlan_taxa. (2022-11-28)
  • fix bugs in run_lefse. (2022-11-28)
  • fix bugs in run_lefse2. (2022-11-28)

XMAS 2.1.7

  • add preprocess_ps including keep taxa in rows, filter taxa whose abundance is zero, fix duplicated tax, replace the taxa NA with the higher level taxa unclassified, filter samples whose library size is zero. (2022-07-20)
  • add check_samples. (2022-07-20)
  • add phyloseq_qc. (2022-07-20)
  • add keep_taxa_in_rows. (2022-07-20)
  • add fix_duplicate_tax. (2022-07-20)
  • add fix_na_tax. (2022-07-20)
  • add convert_taxa_name. (2022-07-20)
  • modify run_cor. (2022-07-20)
  • modify run_partial_cor. (2022-07-20)
  • modify determine_tables. (2022-07-20)
  • modify run_maaslin2. (2022-07-20)
  • modify run_ANOSIM. (2022-07-20)
  • modify core_members. (2022-07-20)
  • modify run_alpha_diversity. (2022-07-20)
  • modify run_beta_diversity. (2022-07-20)
  • modify run_rank_abundance. (2022-07-20)
  • modify run_MantelTest. (2022-07-20)
  • modify run_MRPP. (2022-07-20)
  • modify run_ordination. (2022-07-20)
  • modify run_permanova. (2022-07-20)
  • modify run_RefCheck. (2022-07-20)
  • modify plot_core_taxa. (2022-07-20)
  • modify core_matrix. (2022-07-20)
  • modify plot_StackBarPlot. (2022-07-20)
  • modify aggregate_LOD_taxa. (2022-07-20)
  • modify summarize_taxa. (2022-07-20)
  • modify summarize_LowAbundance_taxa. (2022-07-20)
  • modify run_filter. (2022-07-20)
  • modify run_filter2. (2022-07-20)
  • modify run_filter2. (2022-07-20)
  • fix bugs run_alpha_diversity. (2022-07-21)
  • fix bugs run_beta_diversity. (2022-07-21)
  • fix bugs plot_RankAbundance. (2022-07-21)
  • add parameters run_permanova. (2022-07-21)
  • add parameters run_ANOSIM. (2022-07-21)
  • add parameters run_MRPP. (2022-07-21)
  • add parameters run_alpha_diversity. (2022-07-21)
  • add parameters run_beta_diversity. (2022-07-21)
  • add parameters run_MantelTest. (2022-07-21)
  • add parameters run_permanova. (2022-07-21)
  • modify import_metaphlan_taxa for metaphlan3. (2022-07-22)
  • add run_locom. (2022-07-27)
  • add parameter plot_StackBarPlot. (2022-07-27)
  • modify usage of scripts. (2022-07-27)
  • add ggord. (2022-07-28)
  • modify run_locom. (2022-08-05)
  • modify plot_StackBarPlot. (2022-08-08)
  • add parameters plot_StackBarPlot. (2022-08-08)
  • modify preprocess_ps. (2022-08-08)
  • modify plot_StackBarPlot. (2022-08-11)
  • add useMyCol. (2022-08-11)
  • add annoImage. (2022-08-11)
  • add annoLegend. (2022-08-11)
  • add annoPoint. (2022-08-11)
  • add annoPoint2. (2022-08-11)
  • add annoRect. (2022-08-11)
  • add annoSegment. (2022-08-11)
  • add annoTriangle. (2022-08-11)
  • update plot_StackBarPlot. (2022-08-11)
  • add parameters plot_StackBarPlot. (2022-08-16)
  • update plot_StackBarPlot. (2022-08-22)
  • modify run_filter. (2022-08-23)
  • modify run_filter2. (2022-08-23)
  • modify summarize_LowAbundance_taxa. (2022-08-23)
  • modify summarize_LowAbundance_taxa2. (2022-08-23)
  • modify aggregate_LOD_taxa. (2022-08-23)
  • modify transform_abundances. (2022-08-24)
  • modify aggregate_LOD_taxa. (2022-08-25)
  • update available_ranks. (2022-09-02)
  • update plot_boxplot. (2022-09-02)
  • update plot_barplot. (2022-09-02)
  • update plot_volcano. (2022-09-02)
  • update scripts of differential analysis. (2022-09-02)
  • update plot_volcano for ANCOM results. (2022-09-05)
  • update plot_Ordination for sample annotation. (2022-09-07)
  • update plot_multiple_DA for enriched directory. (2022-09-07)
  • update scripts of differential analysis. (2022-09-07)

XMAS 2.1.6

  • add Gut microbiota Data from Zeybel et al. - 2022. (2022-07-06)
  • add run_cor. (2022-07-06)
  • fix bugs run_lefse. (2022-07-07)
  • add run_partial_cor. (2022-07-08)
  • fix bugs summarize_LowAbundance_taxa. (2022-07-08)
  • fix bugs summarize_taxa. (2022-07-11)
  • add parameter group_number in plot_barplot, plot_boxplot and plot_dotplot. (2022-07-11)
  • change parameter run_RefCheck. (2022-07-11)
  • add plot_correlation_heatmap. (2022-07-12)
  • fix bugs aggregate_LOD_taxa. (2022-07-13)
  • add CA in run_ordination. (2022-07-13)
  • fix bugs summarize_taxa. (2022-07-13)
  • fix bugs plot_Ordination. (2022-07-13)
  • fix bugs summarize_LowAbundance_taxa. (2022-07-14)
  • fix bugs summarize_LowAbundance_taxa2. (2022-07-14)
  • fix bugs plot_StackBarPlot. (2022-07-14)
  • add wes_palette. (2022-07-15)
  • add parameters plot_Ordination. (2022-07-18)
  • add parameters plot_barplot. (2022-07-18)
  • add parameters plot_boxplot. (2022-07-18)
  • add parameters plot_dotplot. (2022-07-18)
  • add parameters plot_Dada2Track. (2022-07-18)
  • add parameters plot_taxa_heatmap. (2022-07-18)
  • add parameters plot_lefse. (2022-07-18)
  • add parameters plot_RankAbundance. (2022-07-18)
  • add parameters plot_topN_boxplot. (2022-07-18)
  • add parameters plot_2DA_venn. (2022-07-18)
  • add parameters plot_volcano. (2022-07-18)
  • add run_lefse2. (2022-07-18)
  • fix bugs determine_tables. (2022-07-19)
  • fix bugs run_lefse. (2022-07-19)
  • fix bugs run_lefse2. (2022-07-19)

XMAS 2.1.5

  • add paired parameter in run_ttest and run_wilcox. (2022-06-27)
  • add Data from Early Childhood Antibiotics and the Microbiome (ECAM) study. (2022-06-27)
  • add run_filter2. (2022-06-29)
  • fix bugs in determine_tables. (2022-06-29)
  • fix bugs in run_RefCheck. (2022-06-30)
  • fix bugs in run_RefCheck. (2022-07-03)
  • modify the scripts’ annotations. (2022-07-05)
  • fix bugs in run_multiple_da. (2022-07-05)
  • fix bugs in run_edger. (2022-07-05)

XMAS 2.1.4

  • fix bugs in plot_Dada2Track and plot_RarefCurve. (2022-06-06)
  • fix bugs in determine_tables. (2022-06-07)
  • format the codes in elegant style. (2022-06-08)
  • fix bugs in import_dada2_taxa. (2022-06-13)
  • fix bugs in run_permanova, run_ANOSIM and run_MRPP. (2022-06-14)
  • fix bugs in get_GroupPhyloseq. (2022-06-14)
  • fix bugs in run_RefCheck. (2022-06-15)
  • fix bugs in scripts, for instance, replacing “SampleID” by “TempRowNames”. (2022-06-15)
  • fix bugs in run_lefse. (2022-06-16)
  • fix bugs in plot_RankAbundance, transform_abundances and run_trim. (2022-06-17)
  • update SchematicFigure in vignettes and README. (2022-06-20)
  • add plot_double_barplot. (2022-06-20)
  • fix bugs in aggregate_LOD_taxa. (2022-06-22)
  • fix bugs in import_metaphlan_taxa. (2022-6-24)

XMAS 2.1.3

  • add aggregate_LOD_taxa and rename scripts. (2022-05-31)

XMAS 2.1.2

  • reassign the packages to imports or suggests. (2022-05-26)

XMAS 2.1.1

  • fix bugs in run_permanova, plot_multiple_DA, summarize_LowAbundance_taxa and plot_boxplot. (2022-05-23)

XMAS 2.1.0

  • add run_mulitple_da and plot_multiple_DA for multiple DA methods’ results. (2022-05-18)

XMAS 2.0.13

  • fix bugs. (2022-05-17)

XMAS 2.0.12

  • Add run_MantelTest. (2022-05-11)
  • Add plot_2DA_venn. (2022-05-11)
  • Modify plot_taxa_heatmap and plot_dotplot. (2022-05-12)
  • Add topN significant taxa boxplot plot_topN_boxplot (2022-05-12)
  • Add run_MRPP. (2022-05-13)
  • Add run_rank_abundance and plot_RankAbundance. (2022-05-13)
  • Add run_impute for imputation. (2022-05-13)

XMAS 2.0.7 (2022-04-12)

  • Add global view modules and other parts.

XMAS 2.0.2 (2022-03-17)

  • Recode the differential analysis scripts run_aldex etc.
  • Modify the import scripts.

XMAS 2.0.1 (2022-03-14)

  • Rearrange the package’s structure.

XMAS 1.0.0 (2021-12-13)

  • The final version 1.0.0.

Initial repository 0.0.1 (2021-07-25)

  • Submitted to gitlab.

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XMAS 2.0 tutorial

https://xbiomeanalysis.github.io/XMAS_tutorial

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