API for Gibbons-Lab/mbtools
Provides helper functions for microbiome preprocessing and analysis

Global functions
.onAttach Source code
ERR260132 Man page
`%p%` Source code
align Source code
align_long_reads Man page Source code
align_short_reads Man page Source code
annotate_contigs Man page
annotate_files Source code
annotate_silva Man page
as.matrix.mbquant Man page Source code
as_phyloseq Man page Source code
association Man page Source code
basecalls Source code
bin_coverage Man page Source code
bracken_to_phyloseq Man page Source code
build_lineage Man page Source code
check_variables Source code
classified_taxa Source code
clean_taxa_names Source code
combinatorial_association Man page Source code
config_align Man page
config_association Man page
config_builder Source code
config_chimera Man page
config_count Man page
config_coverage Man page
config_demultiplex Man page
config_denoise Man page
config_layout Man page
config_parser Source code
config_power Man page
config_preprocess Man page
config_reference Man page
config_rep Man page
config_slimm Man page
config_sra Man page
count_alns Source code
count_med Source code
count_references Man page
demultiplex Man page Source code
denoise Man page Source code
discretize Man page Source code
download_bacterial_transcripts Man page
download_files Man page Source code
download_reads Source code
download_sra Man page Source code
effective_lengths Man page Source code
em_count Man page Source code
entropy Source code
filter_chimeras Source code
filter_counts Man page Source code
filter_reference Man page Source code
find_read_files Man page Source code
find_taxa Man page Source code
getN Source code
get_alignments Source code
get_corncob_pars Source code
get_files Source code
grid Source code
hitdb_cleaner Source code
irep Source code
iter_clr Source code
iter_deseq2 Source code
iter_limma Source code
iter_lm Source code
iter_voom Source code
layout Man page Source code
library_size Source code
mbtools Man page
memory_use Source code
merge_transcripts Man page
mock_plot Man page Source code
mockrobiota Man page Source code
mothur_to_dada Man page Source code
normalize Man page Source code
orlitsky Man page Source code
parse_ensembl_id Man page
parse_threads Source code
plot_bb_fits Man page Source code
plot_counts Man page Source code
plot_entropy Man page
plot_lengths Man page
plot_qualities Man page
plot_taxa Man page Source code
power_analysis Man page
prepare_filelist Source code
preprocess Man page Source code
qualities Source code
quality_control Man page Source code
quality_profile Man page Source code
read_bam Man page Source code
read_blast Man page Source code
read_length Man page Source code
read_slimm Man page Source code
read_slimm_coverage Man page Source code
reads_to_phyloseq Man page Source code
remove_chimeras Man page Source code
remove_reference Man page Source code
replication_rates Man page Source code
select Man page Source code
silent_lib Source code
silva_build_taxonomy Man page
slimm Man page Source code
slimm_files Man page
species_names Source code
split_ext Source code
sra_download_url Source code
sra_filelist Source code
sra_submission Man page Source code
standardize Man page Source code
taxa_count Man page Source code
taxa_metrics Man page Source code
taxa_quants Man page Source code
taxa_str Source code
tool_version Source code
types Man page Source code
unshrink Source code
validate Source code
with_classification Man page Source code
Gibbons-Lab/mbtools documentation built on Jan. 28, 2024, 11:08 a.m.