API for compbiomed/MetaScope
Tools and functions for preprocessing 16S and metagenomic sequencing microbiome data

Global functions
.get_cache Source code
MetaScope Man page
MetaScope-package Man page
add_in_taxa Man page Source code
add_in_taxa_ncbi Man page Source code
add_in_taxa_silva Source code
align_details Man page
align_target Man page Source code
align_target_bowtie Man page Source code
bam_reheader_R Man page Source code
blast_reassignment Man page Source code
blast_result_metrics Man page Source code
blastn_results Man page Source code
blastn_seqs Source code
blastn_single_result Man page Source code
bt2_16S_params Man page
bt2_missing_params Man page
bt2_regular_params Man page
check_blastn_exists Man page Source code
check_samtools_exists Man page Source code
class_taxon Source code
combined_header Man page Source code
comp_line Source code
convert_animalcules Man page Source code
convert_animalcules_patho Man page Source code
convert_animalcules_silva Man page Source code
count_matches Man page Source code
create_MAE Source code
create_qiime_biom Source code
download_genomes Source code
download_parentkingdom Source code
download_refseq Man page Source code
errmessages Source code
extract_reads Man page Source code
fill_in_missing Source code
filter_host Man page Source code
filter_host_bowtie Man page Source code
filter_unmapped_reads Man page Source code
find_accessions Source code
find_strains Source code
get_alignscore Source code
get_assignments Source code
get_children Man page Source code
get_max_index_matrix Source code
get_multi_seqs Man page Source code
get_seqs Man page Source code
get_speciestab Source code
get_table Source code
id_kingdom_rank Source code
identify_rnames Source code
locations Man page Source code
merge_bam_files Man page Source code
meta_demultiplex Man page Source code
metascope_blast Man page Source code
metascope_id Man page
missing_acc_finder Source code
mk_bowtie_index Man page Source code
mk_interim_fastq Source code
mk_subread_index Man page Source code
mk_table Source code
obtain_reads Source code
organize_tax_counts Source code
read_in_id Source code
read_in_id_silva Source code
reduceByYield_RM Source code
reduceByYield_iterate Source code
remove_matches Man page Source code
taxid_to_name Man page Source code
transform_cols Source code
compbiomed/MetaScope documentation built on Nov. 20, 2024, 8 p.m.