metagenomeFeatures: Exploration of marker-gene sequence taxonomic annotations

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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.

Author
Nathan D. Olson, Joseph Nathaniel Paulson, Hector Corrada Bravo
Date of publication
None
Maintainer
Nathan D. Olson <nolson@umiacs.umd.edu>
License
Artistic-2.0
Version
1.4.0
URLs

View on Bioconductor

Man pages

aggregate_taxa
Aggregates a MRexperiment object and returns either an...
annotateFeatures-MgDb-method
Annotating metagenome data with taxonomic information
annotateMRexp_fData-MgDb-method
Annotate MRexperiment object featureData slot using MgDb...
get_demoMgDb
Example MgDb-class object
get_mockMgDb
Mock MgDb-class object
MgDb-class
Metagenome Database class
mgdb_meta
MgDb metadata slot accessor
mgdb_seq
MgDb seq slot accessor
mgdb_taxa
MgDb taxa slot accessor
mgdb_tree
MgDb tree slot accessor
mgFeatures-class
mgFeature-class object
mgF_meta
mgFeatures metadata slot accessor
mgF_seq
mgFeatures refDbSeq slot accessor
mgF_taxa
mgFeatures taxa slot accessor
mgF_tree
mgFeatures refDbTree slot accessor
mgQuery
Example ShortRead 16S experiment dataset
mock_mgF
Example mgFeatures class object
mock_query_df
Example Query Data Frame
reexports
Objects exported from other packages
select-MgDb-method
Querying MgDb objects
show-MgDb-method
Display summary of MgDb-class object
taxa_columns
Column names for MgDb taxonomy slot object
taxa_keys
Taxonomy values for a given keytype
taxa_keytypes
Column names for MgDb taxonomy slot object
taxa_levels
Accessor function for taxonomic levels in MRexperiment...

Files in this package

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