This tutorial was organized according to the XMAS 2.0 functions.
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In the beginning two chapters, we specially provided the basic requirements of bioinformatics and overview on microbiota, and the installation of XMAS.
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In Chapter 3, we convert the results from in-house pipeline into phyloseq-class object for downstream data analysis.
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In Chapter 4 provided the functions to evaluate the data quality.
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In Chapter 5, we introduced the preprocessing methods on microbiota data before differential analysis.
-
In Chapter 6 provided the alpha diversity analysis.
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In Chapter 7 provided the beta diversity analysis.
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In Chapter 8 provided the microbiota composition analysis.
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In Chapter 9 provided the core microbiota analysis.
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In Chapter 10 provided the differential analysis.
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In Chapter 11 provided some functions for visualization.
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In Chapter 12 provided the association analysis.
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In Chapter 13 showed the principals of the differential analysis methods.
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In Chapter 14 provided the examples by using XMAS 2.0 on microbiota data.
- 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
, andplot_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
andplot_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
andplot_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
andrun_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)
- 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 selectingk__Bacteria
. (2022-10-17) - update
aggregate_LOD_taxa
for remainingBRS 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
andrun_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)
- 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)
- 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
andplot_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)
- add paired parameter in
run_ttest
andrun_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)
- fix bugs in
plot_Dada2Track
andplot_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
andrun_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
andrun_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)
- add
aggregate_LOD_taxa
and rename scripts. (2022-05-31)
- reassign the packages to imports or suggests. (2022-05-26)
- fix bugs in
run_permanova
,plot_multiple_DA
,summarize_LowAbundance_taxa
andplot_boxplot
. (2022-05-23)
- add
run_mulitple_da
andplot_multiple_DA
for multiple DA methods’ results. (2022-05-18)
- fix bugs. (2022-05-17)
- Add
run_MantelTest
. (2022-05-11) - Add
plot_2DA_venn
. (2022-05-11) - Modify
plot_taxa_heatmap
andplot_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
andplot_RankAbundance
. (2022-05-13) - Add
run_impute
for imputation. (2022-05-13)
- Add global view modules and other parts.
- Recode the differential analysis scripts
run_aldex
etc. - Modify the import scripts.
- Rearrange the package’s structure.
- The final version 1.0.0.
- Submitted to gitlab.