Store and Transfer Amplicon Sequence Data

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Documentation for package ‘strollur’ version 0.1.2

• DESCRIPTION file
• User guides, package vignettes and other documentation
• Package NEWS
• Package README

Help Pages

abundance	Get the abundance data for sequences, bins, samples, and treatments in a strollur object
add	Add sequences, reports, metadata or resource references to a strollur object
assign	Assign sequence abundances, sequence classifications, bins, bin representative sequences, bin classifications or treatments to a strollur object
clear	clear
copy_dataset	copy_dataset
count	Find the number of sequences, samples, treatments or bins of a given type in a strollur object
export_dataset	export_dataset
get_bin_types	get_bin_types
has_sample	has_sample
has_sequence_strings	has_sequence_strings
import_dataset	Import strollur object from exported data.frame.
is_aligned	is_aligned
is_equal	is_equal
load_dataset	Load strollur object from .rds file
miseq_sop_example	Example strollur object
names	Get the names of various data in a strollur object
new_dataset	new_dataset
new_reference	new_reference
read_dada2	Create a strollur object from dada2 outputs
read_fasta	read_fasta
read_mothur	Create a strollur object from mothur outputs
read_mothur_cons_taxonomy	read_mothur_cons_taxonomy
read_mothur_count	read_mothur_count
read_mothur_list	read_mothur_list
read_mothur_rabund	read_mothur_rabund
read_mothur_shared	read_mothur_shared
read_mothur_taxonomy	read_mothur_taxonomy
read_phyloseq	Create a strollur object from a phyloseq object
read_qiime2	Create a strollur object from a qiime2 outputs
read_qiime2_feature_table	read_qiime2_feature_table
read_qiime2_metadata	read_qiime2_metadata
read_qiime2_taxonomy	read_qiime2_taxonomy
remove_file	remove_file
report	Get a data.frame containing the given report in a strollur object
save_dataset	save_dataset
sort_dataframe	sort_dataframe
strollur	The 'strollur' object stores the data associated with your amplicon sequence analysis.
strollur_example	strollur_example
summary	Summarize the sequences data, custom reports, and scrapped data in a strollur object
unpack_qiime2_artifact	unpack_qiime2_artifact
write_fasta	write_fasta
write_mothur	write_mothur
write_mothur_cons_taxonomy	write_mothur_cons_taxonomy
write_mothur_count	write_mothur_count
write_mothur_design	write_mothur_design
write_mothur_list	write_mothur_list
write_mothur_rabund	write_mothur_rabund
write_mothur_shared	write_mothur_shared
write_phyloseq	write_phyloseq
write_taxonomy	write_taxonomy
xdev_abundance	Get a data.frame containing the requested abundance data
xdev_add_references	Add resource references
xdev_add_report	Add a report to a strollur object
xdev_add_sequences	xdev_add_sequences
xdev_assign_bins	xdev_assign_bins
xdev_assign_bin_representative_sequences	xdev_assign_bin_representative_sequences
xdev_assign_bin_taxonomy	xdev_assign_bin_taxonomy
xdev_assign_sequence_abundance	xdev_assign_sequence_abundance
xdev_assign_sequence_taxonomy	xdev_assign_sequence_taxonomy
xdev_assign_sequence_taxonomy_tidy	xdev_assign_sequence_taxonomy_tidy
xdev_assign_treatments	xdev_assign_treatments
xdev_count	xdev_count
xdev_get_abundances_by_sample	xdev_get_abundances_by_sample
xdev_get_by_sample	xdev_get_by_sample
xdev_get_list_vector	xdev_get_list_vector
xdev_get_sequences	xdev_get_sequences
xdev_has_sequence_taxonomy	xdev_has_sequence_taxonomy
xdev_merge_bins	xdev_merge_bins
xdev_merge_sequences	xdev_merge_sequences
xdev_names	xdev_names
xdev_remove_bins	xdev_remove_bins
xdev_remove_lineages	xdev_remove_lineages
xdev_remove_samples	xdev_remove_samples
xdev_remove_sequences	xdev_remove_sequences
xdev_report	xdev_report
xdev_set_abundance	xdev_set_abundance
xdev_set_abundances	xdev_set_abundances
xdev_set_dataset_name	xdev_set_dataset_name
xdev_set_sequences	xdev_set_sequences