Files in yiluheihei/microbiomeMarker

microbiome biomarker analysis toolkit

.Rbuildignore

.github/.gitignore

.github/ISSUE_TEMPLATE/issue_template.md

.github/workflows/check-bioc.yml

.github/workflows/pkgdown.yaml

.gitignore

DESCRIPTION

LICENSE.md

NAMESPACE

NEWS.md R/AllClasses.R R/AllGenerics.R R/DA-aldex.R R/DA-all.R R/DA-ancom.R R/DA-ancombc.R R/DA-comparing.R R/DA-deseq2.R R/DA-edgeR.R R/DA-lefse.R R/DA-limma-voom.R R/DA-metagenomeSeq.R R/DA-simple-statistic.R R/DA-sl.R R/DA-test-multiple-groups.R R/DA-test-two-groups.R R/abundances-methods.R R/aggregate-taxa.R R/assignment-methods.R R/confounder.R R/data.R R/extract-methods.R R/import-biobakery-lefse_in.R R/import-dada2.R R/import-picrust2.R R/import-qiime2.R R/lefse-utilities.R R/microbiomeMarker.R R/normalization.R R/plot-abundance.R R/plot-cladogram.R R/plot-comparing.R R/plot-effect-size.R R/plot-heatmap.R R/plot-postHocTest.R R/plot-sl-roc.R R/post-hoc-test.R R/reexports.R R/subset-marker.R R/summarize-taxa.R

R/sysdata.rda

R/test-utilities.R R/transform.R R/utilities.R README.Rmd README.md

_pkgdown.yml

codecov.yml

data-raw/available_ranks.R data-raw/data.R

data/caporaso.rda

data/cid_ying.rda

data/ecam.rda

data/enterotypes_arumugam.rda

data/kostic_crc.rda

data/oxygen.rda

data/pediatric_ibd.rda

data/spontaneous_colitis.rda

inst/CITATION

inst/extdata/dada2_samdata.txt

inst/extdata/dada2_seqtab.rds

inst/extdata/dada2_taxtab.rds

inst/extdata/path_abun_unstrat_descrip.tsv.gz

inst/extdata/picrust2_metadata.tsv

inst/extdata/refseq.qza

inst/extdata/sample-metadata.tsv

inst/extdata/table.qza

inst/extdata/taxonomy.qza

inst/extdata/tree.qza

man/abundances-methods.Rd man/aggregate_taxa.Rd man/assign-marker_table.Rd man/assign-otu_table.Rd man/compare_DA.Rd man/confounder.Rd man/data-caporaso.Rd man/data-cid_ying.Rd man/data-ecam.Rd man/data-enterotypes_arumugam.Rd man/data-kostic_crc.Rd man/data-oxygen.Rd man/data-pediatric_ibd.Rd man/data-spontaneous_colitis.Rd man/effect_size-plot.Rd man/extract-methods.Rd man/extract_posthoc_res.Rd

man/figures/microbiome.png

man/figures/microbiomeMarker.png

man/figures/sticker.R man/get_treedata_phyloseq.Rd man/import_dada2.Rd man/import_picrust2.Rd man/import_qiime2.Rd man/marker_table-class.Rd man/marker_table-methods.Rd man/microbiomeMarker-class.Rd man/microbiomeMarker-package.Rd man/microbiomeMarker.Rd man/nmarker-methods.Rd man/normalize-methods.Rd man/phyloseq2DESeq2.Rd man/phyloseq2edgeR.Rd man/phyloseq2metagenomeSeq.Rd man/plot.compareDA.Rd man/plot_abundance.Rd man/plot_cladogram.Rd man/plot_heatmap.Rd man/plot_postHocTest.Rd man/plot_sl_roc.Rd man/postHocTest-class.Rd man/postHocTest.Rd man/reexports.Rd man/run_aldex.Rd man/run_ancom.Rd man/run_ancombc.Rd man/run_deseq2.Rd man/run_edger.Rd man/run_lefse.Rd man/run_limma_voom.Rd man/run_marker.Rd man/run_metagenomeseq.Rd man/run_posthoc_test.Rd man/run_simple_stat.Rd man/run_sl.Rd man/run_test_multiple_groups.Rd man/run_test_two_groups.Rd man/subset_marker.Rd man/summarize_taxa.Rd man/summary.compareDA.Rd man/transform_abundances.Rd tests/testthat.R tests/testthat/_snaps/ancom.md tests/testthat/_snaps/edgeR.md tests/testthat/_snaps/lefse.md tests/testthat/_snaps/limma-voom.md tests/testthat/_snaps/multiple-groups-test.md tests/testthat/_snaps/two-group-test.md

tests/testthat/data/ancom-zero.csv

tests/testthat/data/ancom-zero_neg_lb.csv

tests/testthat/data/data_tax_duplicate.rds

tests/testthat/data/generate_cladogram_annotation.rds

tests/testthat/test-abundances.R tests/testthat/test-aldex.R tests/testthat/test-ancom.R tests/testthat/test-ancombc.R tests/testthat/test-assignment.R tests/testthat/test-barplot.R tests/testthat/test-comparing.R tests/testthat/test-confounder.R tests/testthat/test-edgeR.R tests/testthat/test-extract.R tests/testthat/test-import-picrust2.R tests/testthat/test-import-qiime2.R tests/testthat/test-lefse-input.R tests/testthat/test-lefse.R tests/testthat/test-limma-voom.R tests/testthat/test-metagenomeSeq.R tests/testthat/test-microbiomeMaker-methods.R tests/testthat/test-microbiomeMarker-class.R tests/testthat/test-multiple-groups-test.R tests/testthat/test-normalization.R tests/testthat/test-sl.R tests/testthat/test-summarize-tax.R tests/testthat/test-transform.R tests/testthat/test-two-group-test.R tests/testthat/test-utilities.R tests/testthat/test_cladogram.R tests/testthat/test_fix_duplicate_tax.R

vignettes/.gitignore

vignettes/microbiomeMarker-vignette.Rmd

vignettes/vignette.bib

yiluheihei/microbiomeMarker documentation built on Nov. 5, 2023, 7:19 a.m.