metagenomeFeatures: Exploration of marker-gene sequence taxonomic annotations

metagenomeFeatures was developed for use in exploring the taxonomic annotations for a marker-gene metagenomic sequence dataset. The package can be used to explore the taxonomic composition of a marker-gene database or annotated sequences from a marker-gene metagenome experiment.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("metagenomeFeatures")
AuthorNathan D. Olson, Joseph Nathaniel Paulson, Hector Corrada Bravo
Bioconductor views Annotation Infrastructure Metagenomics Microbiome Sequencing Software
Date of publicationNone
MaintainerNathan D. Olson <nolson@umiacs.umd.edu>
LicenseArtistic-2.0
Version1.8.0
https://github.com/HCBravoLab/metagenomeFeatures

View on Bioconductor

Functions

\%>\% Man page
aggregate_taxa Man page
annotateFeatures Man page
annotateFeatures,MgDb-method Man page
annotateMRexp_fData Man page
annotateMRexp_fData,MgDb-method Man page
get_demoMgDb Man page
get_mockMgDb Man page
mgdb Man page
MgDb Man page
MgDb-class Man page
mgdb_meta Man page
mgDb_select Man page
mgDb_select,MgDb-method Man page
mgdb_seq Man page
mgdb_taxa Man page
mgdb_tree Man page
mgFeatures-class Man page
mgF_meta Man page
mgF_seq Man page
mgF_taxa Man page
mgF_tree Man page
mgQuery Man page
mock_mgF Man page
mock_query_df Man page
reexports Man page
select,MgDb-method Man page
show,MgDb-method Man page
taxa_columns Man page
taxa_columns,MgDb-method Man page
taxa_keys Man page
taxa_keys,MgDb-method Man page
taxa_keytypes Man page
taxa_keytypes,MgDb-method Man page
taxa_levels Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/aggregate_taxa.R R/demoMgDb.R R/mgDb-class.R R/mgDb-taxa_accessors.R R/mgDb_method_annotateFeatures.R R/mgDb_method_annotateMRexp.R R/mgDb_method_select.R R/mgFeatures-class.R R/mgQuery.R R/mockMgDb.R R/mock_mgF.R R/mock_query_df.R R/phylo-class.R R/utils.R R/vignette_data.R
README.md
build
build/vignette.rds
data
data/mgQuery.rdata
data/mock_mgF.RData
data/mock_query_df.rdata
inst
inst/doc
inst/doc/Example_16S_Annotation_Workflow.R
inst/doc/Example_16S_Annotation_Workflow.Rmd
inst/doc/Example_16S_Annotation_Workflow.html
inst/doc/Exploring_a_MgDb.R
inst/doc/Exploring_a_MgDb.Rmd
inst/doc/Exploring_a_MgDb.html
inst/extdata
inst/extdata/6692_analysis_dt-16S_r-1_c-3.biom
inst/extdata/demoSeq.fasta.gz
inst/extdata/demoTaxa.sqlite
inst/extdata/genus_keys.RData
inst/extdata/gg_rep_genus_df.csv
inst/extdata/mockSeq.fasta.gz
inst/extdata/mockTaxa.sqlite
inst/extdata/mockTree.rds
inst/extdata/mockTree.tree
inst/extdata/mock_MgDb_seq.fasta.gz
inst/extdata/mock_MgDb_taxa.sqlite
inst/extdata/mock_counts.csv
inst/extdata/mock_sample_data.csv
inst/extdata/msd16s_MgDb_tree.rds
inst/scripts
inst/scripts/make_mockMgDb.R inst/scripts/make_mock_mgF.R inst/scripts/make_mock_query_df.R inst/scripts/make_testMgAnno.R inst/scripts/make_testMgDb.R
man
man/MgDb-class.Rd man/aggregate_taxa.Rd man/annotateFeatures-MgDb-method.Rd man/annotateMRexp_fData-MgDb-method.Rd man/get_demoMgDb.Rd man/get_mockMgDb.Rd man/mgF_meta.Rd man/mgF_seq.Rd man/mgF_taxa.Rd man/mgF_tree.Rd man/mgFeatures-class.Rd man/mgQuery.Rd man/mgdb_meta.Rd man/mgdb_seq.Rd man/mgdb_taxa.Rd man/mgdb_tree.Rd man/mock_mgF.Rd man/mock_query_df.Rd man/reexports.Rd man/select-MgDb-method.Rd man/show-MgDb-method.Rd man/taxa_columns.Rd man/taxa_keys.Rd man/taxa_keytypes.Rd man/taxa_levels.Rd
tests
tests/testMgAnno.rds
tests/testSeq.fasta.gz
tests/testTaxa.sqlite3
tests/test_seq.rds
tests/test_taxa.sqlite3
tests/test_tree.rds
tests/testthat
tests/testthat.R
tests/testthat/cache
tests/testthat/cache/MgDb_test_annotate.rds
tests/testthat/cache/MgDb_test_annotateMRexp.rds
tests/testthat/cache/MgDb_test_select_both.rds
tests/testthat/cache/MgDb_test_select_seq.rds
tests/testthat/cache/MgDb_test_select_taxa.rds
tests/testthat/cache/MgDb_test_taxa_columns.rds
tests/testthat/cache/MgDb_test_taxa_keys_Class.rds
tests/testthat/cache/MgDb_test_taxa_keys_Family.rds
tests/testthat/cache/MgDb_test_taxa_keys_Genus.rds
tests/testthat/cache/MgDb_test_taxa_keys_Kingdom.rds
tests/testthat/cache/MgDb_test_taxa_keys_Kingdom_Species.rds
tests/testthat/cache/MgDb_test_taxa_keys_Order.rds
tests/testthat/cache/MgDb_test_taxa_keys_Phylum.rds
tests/testthat/cache/MgDb_test_taxa_keys_Species.rds
tests/testthat/cache/MgDb_test_taxa_keytypes.rds
tests/testthat/cache/metagenomeAnnotation_split_by_Class.rds
tests/testthat/cache/metagenomeAnnotation_split_by_Family.rds
tests/testthat/cache/metagenomeAnnotation_split_by_Genus.rds
tests/testthat/cache/metagenomeAnnotation_split_by_Kingdom.rds
tests/testthat/cache/metagenomeAnnotation_split_by_Order.rds
tests/testthat/cache/metagenomeAnnotation_split_by_Phylum.rds
tests/testthat/cache/metagenomeAnnotation_split_by_Species.rds
tests/testthat/helper-MRexp.R tests/testthat/helper-MgDb.R tests/testthat/test_MRexp_anno.R tests/testthat/test_agg_tax.R tests/testthat/test_mdDb-annotateFeatures.R tests/testthat/test_metagenomeAnnotation-class.R tests/testthat/test_mgDb-class.R tests/testthat/test_mgDb-select.R tests/testthat/test_mgFeatures-class.R tests/testthat/test_vignette_data.R
vignettes
vignettes/Example_16S_Annotation_Workflow.Rmd
vignettes/Exploring_a_MgDb.Rmd

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