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 | 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 |
