Files in waldronlab/curatedMetagenomicData
Curated Metagenomic Data of the Human Microbiome

.Rbuildignore
.gitignore
.travis.yml
CONTRIBUTING.md
DESCRIPTION
LICENSE
NAMESPACE
NEWS
R/AsnicarF_2017.R R/BritoIL_2016.R R/Castro-NallarE_2015.R R/ChngKR_2016.R R/ExpressionSet2MRexperiment.R R/ExpressionSet2phyloseq.R R/FengQ_2015.R R/HMP_2012.R R/HanniganGD_2017.R R/Heitz-BuschartA_2016.R R/KarlssonFH_2013.R R/LeChatelierE_2013.R R/LiJ_2014.R R/LiuW_2016.R R/LomanNJ_2013.R R/NielsenHB_2014.R R/Obregon-TitoAJ_2015.R R/OhJ_2014.R R/QinJ_2012.R R/QinN_2014.R R/RampelliS_2015.R R/RaymondF_2016.R R/SchirmerM_2016.R R/TettAJ_2016.R R/VatanenT_2016.R R/VincentC_2016.R R/VogtmannE_2016.R R/XieH_2016.R R/YuJ_2015.R R/ZellerG_2014.R R/combined_metadata.R R/curatedMetagenomicData-package.R R/curatedMetagenomicData.R R/getMetaphlanTree.R R/mergeData.R R/versioning.R R/zzz.R README.md
appveyor.yml
codecov.yml
curatedMetagenomicData.Rproj
data-raw/add_version_number.R data-raw/assay_merge.R data-raw/author_df.R data-raw/author_str.R data-raw/bodysite_eset.R data-raw/cat_documentation.R data-raw/combine_metadata.R data-raw/create_dir.R data-raw/description_str.R data-raw/documentation_aliases.R data-raw/documentation_datasets.R data-raw/documentation_eda.R data-raw/documentation_examples.R data-raw/documentation_filename.R data-raw/documentation_format.R data-raw/documentation_name.R data-raw/documentation_section.R data-raw/documentation_source.R data-raw/documentation_title.R data-raw/drop_rows.R data-raw/eset_name.R data-raw/feature_number.R data-raw/figure_bar.R data-raw/figure_density.R data-raw/fix_colnames.R data-raw/fix_rownames.R data-raw/format_dataset_name.R data-raw/format_experiment_data.R data-raw/format_metadata.R data-raw/format_pheno_data.R data-raw/genefamilies_relab.R data-raw/get_Description.R data-raw/get_DispatchClass.R data-raw/get_Tags.R data-raw/get_aliases.R data-raw/get_dataset_dir.R data-raw/get_documentation.R data-raw/get_experiment_data.R data-raw/get_metadata.R data-raw/get_name.R data-raw/get_resource.R data-raw/get_subsection.R data-raw/get_technology.R data-raw/get_title.R data-raw/guess_cols.R data-raw/has_header.R data-raw/is_rda.R data-raw/join_assays.R data-raw/make_all.R data-raw/make_data.R data-raw/make_data_documentation.R data-raw/make_metadata.R data-raw/make_metadata_documentation.R data-raw/make_upload.R data-raw/marker_abundance.R data-raw/marker_presence.R data-raw/merged_eset.R data-raw/metadata_cols.R data-raw/metaphlan_bugs_list.R data-raw/miame_lab.R data-raw/miame_name.R data-raw/miame_other.R data-raw/na_zero.R data-raw/name_str.R data-raw/parallel_rbind.R data-raw/pathabundance_relab.R data-raw/pathcoverage.R data-raw/pheno_order.R data-raw/pubmed_check.R data-raw/pubmed_query.R data-raw/read_assay.R data-raw/read_sample.R data-raw/rownames_match.R data-raw/sample_name.R data-raw/sample_number.R data-raw/save_eset.R data-raw/subsection_str.R data-raw/title_str.R data-raw/write_documentation.R
data/combined_metadata.rda
docs/.gitignore
docs/404.md
docs/Gemfile
docs/Gemfile.lock
docs/LICENSE
docs/README.md
docs/_config.yml
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docs/_layouts/post.html
docs/_posts/2017-06-06-contributing-analyses.md docs/_posts/2017-06-06-package-vignette.md docs/_posts/2017-06-06-paper-figures.md docs/analyses.md
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docs/assets/ppt/2016-11-24_Columbia_curatedMetagenomicData.pptx
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docs/config.rb
docs/credits.md docs/datasets-included.md docs/datasets-ongoing.md
docs/feed.xml
docs/getting-started.md docs/index.md docs/publications.md
inst/CITATION
inst/commandline/README.md
inst/commandline/curatedMetagenomicData
inst/docker/curatedMetagenomics/Dockerfile
inst/docker/curatedMetagenomics/README.md
inst/docker/curatedMetagenomics/curatedMetagenomicData_pipeline.sh
inst/docker/curatedMetagenomics/run_markers2.py
inst/docker/sratoolkit/Dockerfile
inst/extdata/curatedMetagenomicData.txt
inst/extdata/metadata.csv
inst/extdata/metaphlan2_selected.tree.reroot.nwk.bz2
inst/extdata/template.csv
inst/extdata/versions.txt
inst/pipeline/README.md
inst/pipeline/curatedMetagenomicData_pipeline.sh
inst/pipeline/curatedMetagenomicData_pipeline_allsamples.sh
inst/pipeline/run_markers2.py
inst/scripts/make-data.R inst/scripts/make-metadata.R
inst/wdl/metaphlan_from_sra.wdl
man/AsnicarF_2017.Rd man/BritoIL_2016.Rd man/Castro-NallarE_2015.Rd man/ChngKR_2016.Rd man/ExpressionSet2MRexperiment.Rd man/ExpressionSet2phyloseq.Rd man/FengQ_2015.Rd man/HMP_2012.Rd man/HanniganGD_2017.Rd man/Heitz-BuschartA_2016.Rd man/KarlssonFH_2013.Rd man/LeChatelierE_2013.Rd man/LiJ_2014.Rd man/LiuW_2016.Rd man/LomanNJ_2013.Rd man/NielsenHB_2014.Rd man/Obregon-TitoAJ_2015.Rd man/OhJ_2014.Rd man/QinJ_2012.Rd man/QinN_2014.Rd man/RampelliS_2015.Rd man/RaymondF_2016.Rd man/SchirmerM_2016.Rd man/TettAJ_2016.Rd man/VatanenT_2016.Rd man/VincentC_2016.Rd man/VogtmannE_2016.Rd man/XieH_2016.Rd man/YuJ_2015.Rd man/ZellerG_2014.Rd man/cmdValidVersions.Rd man/combined_metadata.Rd man/curatedMetagenomicData.Rd
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man/getMetaphlanTree.Rd man/mergeData.Rd tests/testthat.R tests/testthat/test-ExpressionSet2MRexperiment.R tests/testthat/test-ExpressionSet2phyloseq.R tests/testthat/test-HiddenFunctions.R tests/testthat/test-cmdValidVersions.R tests/testthat/test-curatedMetagenomicData.R tests/testthat/test-mergeData.R vignettes/curatedMetagenomicData.Rmd vignettes/extras/PaperFigures.Rmd vignettes/extras/PaperFigures.knit.md
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waldronlab/curatedMetagenomicData documentation built on Jan. 9, 2018, 1:48 a.m.