HuaZou/MicrobiomeAnalysis
Data analysis toolkits in metagenomics

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Functions
325
Source code
50
Man pages
80
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HuaZou/MicrobiomeAnalysis: Data analysis toolkits in metagenomics
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API

API for HuaZou/MicrobiomeAnalysis
Data analysis toolkits in metagenomics

Global functions
%>% Man page
.Calculate_LowAbundance_taxa Source code
.GlobalMean Source code
.SVD_wrapper Source code
.cal_variable_distance Source code
.import_dada2_taxa Source code
.one_permanova Source code
.scale_recover Source code
.sum_consensus Source code
.summarize_taxa_level Source code
DA_FoldChange Source code
DA_VIP Source code
DA_mergedResults Source code
DA_ttest Source code
LowAbundance_taxa Source code
Zeybel_2022_gut Man page
Zeybel_2022_gut_paired Man page
Zeybel_2022_metabolite Man page
Zeybel_2022_metabolite_paired Man page
Zeybel_2022_oral Man page
Zeybel_2022_oral_paired Man page
Zeybel_2022_protein Man page
Zeybel_2022_protein_paired Man page
[ Man page
[,marker_table,ANY,ANY,ANY-method Man page
abundances Man page
abundances, Man page
abundances,SummarizedExperiment-method Man page
abundances,assay-method Man page
abundances,microbiomeMarker-method Man page
abundances,otu_table-method Man page
abundances,phyloseq-method Man page
add_missing_levels Source code
add_prefix Source code
add_prefix_summarized Source code
aggregate_taxa Man page Source code
aldex_kw Source code
aldex_t Source code
arrange Man page
assay-method Man page
assign-marker_table Man page
assign-otu_table Man page
bootstap_lda Source code
bootstap_lda_one Source code
bootstrap_diff_mean_prop_single Source code
cal_pair_lda Source code
calc_ancom_p Source code
calc_ancom_pmat Source code
calc_bootstrap_ci Source code
calc_coef Source code
calc_ef_md_f Source code
calc_p_large_sample Source code
calc_permute_p Source code
calc_permute_ts Source code
calc_ratio Source code
calc_sparse_diff_mean Source code
calc_sparse_p Source code
calc_twosample_ts Source code
calc_twosample_ts_single_feature Source code
calculate_MeanRank_abundance Man page Source code
calculate_geometricmean_abundance Man page Source code
calculate_mean_abundance Man page Source code
calculate_median_abundance Man page Source code
calculate_occurrence_taxa Man page Source code
caporaso Man page
check_bootstrap_sample Source code
check_confounder Source code
check_contrast Source code
check_rank_names Source code
check_sample_names Man page Source code
check_samples Source code
check_tax_prefix Source code
check_tax_summarize Source code
check_taxa_rank Source code
check_var_in_meta Source code
confounder Man page Source code
convert_instance Source code
count Man page
create_contingency_matrix Source code
create_contrast Source code
create_design Source code
create_pairwise_contrast Source code
create_ps_from_mm Source code
data-Zeybel_2022_gut Man page
data-Zeybel_2022_gut_paired Man page
data-Zeybel_2022_metabolite Man page
data-Zeybel_2022_metabolite_paired Man page
data-Zeybel_2022_oral Man page
data-Zeybel_2022_oral_paired Man page
data-Zeybel_2022_protein Man page
data-Zeybel_2022_protein_paired Man page
data-caporaso Man page
data-ecam Man page
data-enterotypes_arumugam Man page
default_color Man page Source code
distinct Man page
ecam Man page
enterotypes_arumugam Man page
estimateSizeFactorsForMatrix Source code
extract_prefix Source code
extract_rank Source code
filter Man page
filter_abundance Man page Source code
fix_duplicate_tax Source code
fix_na_tax Source code
geom_enterotype Source code
get_GUniFrac Man page Source code
get_aldex_kwglm_enrich_group Source code
get_alphaindex Man page Source code
get_ancom_enrich_group Source code
get_ancombc_enrich_group Source code
get_available_prefix Source code
get_eigValue Man page Source code
get_feature_enrich_group Source code
get_mgs_enrich_group Source code
get_norm_factors Source code
get_norm_method Source code
get_prefix Source code
get_sl_enrich_group Source code
get_struc_zero Source code
gm_mean Source code
group_by Man page
has_prefix Source code
import_SE Man page Source code
import_biom Man page
import_dada2 Man page Source code
import_mothur Man page
import_qiime Man page
import_qiime2 Man page Source code
impute_abundance Man page Source code
insertCol Man page
insertRow Man page
is_dna_seq Source code
is_picrust2 Source code
keep_prefix_desc Source code
keep_taxa_in_rows Source code
lag Man page
lefse_format_grp Source code
left_join Man page
marker_table Man page
marker_table,data.frame-method Man page
marker_table,microbiomeMarker-method Man page
marker_table-class Man page
marker_table<- Man page
microbiomeMarker Man page Source code
microbiomeMarker-class Man page
mutate Man page
nmarker Man page
nmarker,marker_table-method Man page
nmarker,microbiomeMarker-method Man page
norm_clr Man page Source code
norm_cpm Man page Source code
norm_css Man page Source code
norm_rarefy Man page Source code
norm_rle Man page Source code
norm_tmm Man page Source code
norm_tss Man page Source code
normalize Man page
normalize,data.frame-method Man page
normalize,matrix-method Man page
normalize,otu_table-method Man page
normalize,phyloseq-method Man page
normalize_feature Source code
nsamples Man page
ntaxa Man page
otu_table Man page
otu_table-method Man page
otu_table2metagenomeSeq Man page Source code
otu_table<-,microbiomeMarker,microbiomeMarker-method Man page
otu_table<-,microbiomeMarker,otu_table-method Man page
otu_table<-,microbiomeMarker,phyloseq-method Man page
parse_q2taxonomy Source code
phyloseq2DESeq2 Man page Source code
phyloseq2edgeR Man page Source code
phyloseq2metagenomeSeq Man page Source code
phyloseq_qc Source code
plot_ord Man page Source code
plot_volcano Man page Source code
postHocTest Man page Source code
postHocTest-class Man page
postHocTest-method Man page
pre_ps_taxa_rank Source code
preprocess_ancom Source code
preprocess_feature Source code
preprocess_feature_all Source code
preprocess_ps Source code
pull Man page
read_q2biom Source code
read_q2sample_meta Source code
read_q2taxa Source code
read_qza Source code
reexports Man page
remove_na_samples Source code
rename Man page
return_marker Source code
run_ANOSIM Man page Source code
run_CI Man page
run_MANTEL Man page Source code
run_MRPP Man page Source code
run_OddRatio Man page Source code
run_PERMANOVA Man page Source code
run_STDERR Man page
run_aldex Man page Source code
run_ancom Man page Source code
run_ancombc Man page Source code
run_betadisper Man page Source code
run_deseq2 Man page Source code
run_distance Man page Source code
run_edger Man page Source code
run_group.CI Man page
run_group.STDERR Man page
run_lefse Man page Source code
run_limma_voom Man page Source code
run_marker Man page Source code
run_metabolomeDA Man page Source code
run_metagenomeseq Man page Source code
run_ord Man page Source code
run_simple_stat Man page Source code
run_sl Man page Source code
run_summarySE Man page
run_t_test Source code
run_test_multiple_groups Man page Source code
run_test_two_groups Man page Source code
run_white_test Source code
sample_data Man page
sample_names Man page
scale_MeanCenter Source code
scale_Pareto Source code
scale_Range Source code
scale_Zscore Source code
scale_variables Man page Source code
select Man page
select_quantile_func Source code
set_lvl Source code
set_nf Source code
show, Man page
show,microbiomeMarker-method Man page
show,postHocTest-method Man page
slice Man page
space Source code
subset_marker Man page Source code
subset_taxa_in_feature Source code
summarize_taxa Man page Source code
t_fast Source code
tax_table Man page
taxa_names Man page
test_rep_wilcoxon Source code
trans_clr Source code
transform_CubicRoot Source code
transform_SquareRoot Source code
transform_abundances Man page Source code
transform_log10 Source code
transform_log10p Source code
transform_log2 Source code
transform_log2p Source code
transform_logit Source code
transpose_and_2df Source code
trim_FeatureByGroup Source code
trim_FeatureOrSample Source code
trim_prevalence Man page Source code
ungroup Man page
upper_firstletter Source code
validity_marker_table Source code
validity_microbiomeMarker Source code
validity_postHocTest Source code
wilcox_fast Source code
HuaZou/MicrobiomeAnalysis documentation built on Dec. 12, 2023, 10:37 a.m.

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