Files in rusher321/microbiotaPair
An R Package for Simplified Microbiome Analysis Workflows on Intervention Study
.Rbuildignore
.gitignore
DESCRIPTION
MicroPair/globalview/alpha.csv
MicroPair/globalview/alpha.figre.pdf
NAMESPACE
R/Wilcoxon_Sign_Rank_Test.R
R/alpha_diversity.R
R/basic.R
R/config.R
R/convert_data_into_phyloseq.R
R/generalized_estimating_equations.R
R/group_distance.R
R/main.script.R
R/mantel_test.R
R/network.R
R/ordination.R
R/pair_foldchange.R
R/pcorPair.R
R/permanova.R
R/plot_alpha_diversity.R
R/plot_central_distance.R
R/plot_ordination.R
R/predict.R
R/two_part_compare.R
README.md
data/grid.merged.reliable.tsv
data/humann2.uniref90_ko.joined_unstratified.tsv
data/humann2_pathabundance_joined_unstratified.tsv
data/metadata.xlsx
data/metaphlan2.rankclass.tab
data/metaphlan3.merged.abundance.profile.all.tsv
data/microbioP.png
data/microbiota.png
data/physeq_data.rda
example/PMV.Rmd
example/PMV.nb.html
example/clinical.pathway.pcor.pdf
example/clinical.pathway.spearman.pdf
example/clinical.species.pcor.pdf
example/clinical.species.spearman.pdf
example/clinical_pathway_pcor.xlsx
example/clinical_pathway_spearman.xlsx
example/clinical_species_pcor.csv
example/clinical_species_spearman.csv
example/g0_igraph.csv
example/g0_network.pdf
example/genus_compare.csv
example/humann2_compare.csv
example/species_compare.csv
inst/extdata/abundance.profile
inst/extdata/metabolic.profile
inst/extdata/phenotype.csv
man/CvLasso.Rd
man/LassoFeatruePlot.Rd
man/PERMANOVA1.Rd
man/PcorPair.Rd
man/alpha_diversity.Rd
man/compare_two.Rd
man/comtaxTop.Rd
man/data2phyloseq.Rd
man/filterEx.Rd
man/filterPer.Rd
man/gee_test.Rd
man/ggiNEXT.Rd
man/hill_number.Rd
man/mantel_test.Rd
man/multiplot.Rd
man/network_sta.Rd
man/network_tran.Rd
man/ordination.Rd
man/pairNet.Rd
man/pair_foldchange.Rd
man/perfPlot.Rd
man/plot_alpha_diversity.Rd
man/plot_centrel.Rd
man/plot_ordination.Rd
man/plot_pair_distance.Rd
man/randomForestTwo.Rd
man/randomForestTworobust.Rd
man/repeatNetwork.Rd
man/rocPlot2.Rd
man/simplenet.Rd
man/sparCCnetwork.Rd
man/sparccNet.Rd
man/two_part_compare.Rd
microbiotaPair.Rproj
