Man pages for compbiomed/MetaScope
Tools and functions for preprocessing 16S and metagenomic sequencing microbiome data
| add_in_taxa | Adds in taxa if silva database Returns MetaScope Table with... |
| add_in_taxa_ncbi | Adds in taxa if input used NCBI database |
| align_details | A universal parameter settings object for Rsubread alignment |
| align_target | Align microbiome reads to a set of reference libraries |
| align_target_bowtie | Align microbiome reads to set of indexed Bowtie2 libraries |
| bam_reheader_R | Replace the header from a .bam file |
| blastn_results | Reformat BLASTn results |
| blastn_single_result | blastn_single_result |
| blast_reassignment | Reassign reads from MetaScope BLASTn alignment |
| blast_result_metrics | Calculates result metrics from a blast results table |
| bt2_16S_params | A universal parameter object for Bowtie 2 16S alignment |
| bt2_missing_params | A universal parameter object for Bowtie 2 metagenomic... |
| bt2_regular_params | A universal parameter object for Bowtie 2 metagenomic or... |
| check_blastn_exists | Check if blastn exists on the system |
| check_samtools_exists | Check if samtools exists on the system |
| combined_header | Create a combined .bam header |
| convert_animalcules | Create a multi-assay experiment from MetaScope output for... |
| convert_animalcules_patho | Create a multi-assay experiment from PathoScope 2.0 output... |
| convert_animalcules_silva | Create a multi-assay experiment from MetaScope output for... |
| count_matches | Count the number of base lengths in a CIGAR string for a... |
| download_accessions | Download indexes required for MetaScope ID and MetaBlast... |
| download_refseq | Download RefSeq genome libraries |
| extract_reads | Helper function for demultiplexing |
| filter_host | Use Rsubread to align reads against one or more filter... |
| filter_host_bowtie | Use Rbowtie2 to align reads against one or more filter... |
| filter_unmapped_reads | Filter unmapped reads |
| get_children | Get child nodes from NCBI taxonomy |
| get_multi_seqs | Gets multiple sequences from different accessions in a bam... |
| get_seqs | Gets sequences from bam file |
| locations | Helper Function for MetaScope ID |
| merge_bam_files | Merge multiple .bam files |
| meta_demultiplex | Demultiplexing sequencing reads |
| metascope_blast | Blast reads from MetaScope aligned files |
| metascope_id | Identify which genomes are represented in a processed sample |
| MetaScope-package | MetaScope: Tools and functions for preprocessing 16S and... |
| mk_bowtie_index | Make a Bowtie2 index |
| mk_subread_index | Make a Subread index |
| remove_matches | Helper function to remove reads matched to filter libraries |
| taxid_to_name | Converts NCBI taxonomy ID to scientific name |
