Function reference
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download_refseq()
- Download RefSeq genome libraries
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demultiplex()
- Demultiplexing sequencing reads
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mk_bowtie_index()
- Make a Bowtie2 index
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mk_subread_index()
- Make a Subread index
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align_target()
- Align microbiome reads to a set of reference libraries
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filter_host()
- Use Rsubread to align reads against one or more filter libraries and subsequently remove mapped reads
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align_details
- A universal parameter settings object for Rsubread alignment
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align_target_bowtie()
- Align microbiome reads to set of indexed Bowtie2 libraries
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filter_host_bowtie()
- Use Rbowtie2 to align reads against one or more filter libraries and subsequently remove mapped reads
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bt2_16S_params
- A universal parameter object for Bowtie 2 16S alignment
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bt2_loose_params
- A universal parameter object for Bowtie 2 loose alignment
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metascope_id()
- Identify which genomes are represented in a processed sample
Downstream Analysis with animalcules
Convert MetaScope output to be compatible with the animalcules R package.
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convert_animalcules()
- Create a multi-assay experiment from MetaScope output for usage with animalcules
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remove_matches()
- Helper function to remove reads matched to filter libraries
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combined_header()
- Create a combined .bam header
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bam_reheader_R()
- Replace the header from a .bam file
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get_children()
- Get child nodes from NCBI taxonomy
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merge_bam_files()
- Merge multiple .bam files
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count_matches()
- Count the number of base lengths in a CIGAR string for a given operation
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extract_reads()
- Helper function for demultiplexing
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locations()
- Helper Function for MetaScope ID
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filter_unmapped_reads()
- Filter unmapped reads
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check_samtools_exists()
- Check if samtools exists on the system