Package: MetaScope 2.0.0

Sean Lu

MetaScope: Tools and functions for preprocessing 16S and metagenomic sequencing microbiome data

This package contains tools and methods for preprocessing microbiome data. Functionality includes library generation, demultiplexing, alignment, and microbe identification. It is in part an R translation of the PathoScope 2.0 pipeline.

Authors:Sean Lu [aut, cre], Aubrey Odom [aut], Rahul Varki [aut], W. Evan Johnson [aut]

MetaScope_2.0.0.tar.gz
MetaScope_2.0.0.tar.gz(r-4.7-any)MetaScope_2.0.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
MetaScope/json (API)

# Install 'MetaScope' in R:

install.packages('MetaScope', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/wejlab/metascope/issues

Pkgdown/docs site:https://wejlab.github.io

Datasets:

align_details - A universal parameter settings object for Rsubread alignment
bt2_16S_params - A universal parameter object for Bowtie 2 16S alignment
bt2_missing_params - A universal parameter object for Bowtie 2 metagenomic alignment where the host genome is thought to be absent from the reference database
bt2_regular_params - A universal parameter object for Bowtie 2 metagenomic or non-16S alignment

On BioConductor:MetaScope-2.1.0(data/experiment 3.24)MetaScope-2.0.0(data/experiment 3.23)

microbiomedata reproducibleresearch sequencingdata datapkg

6.74 score 22 stars 18 scripts 22 exports 89 dependencies

Last updated from:1f2155fa36 (on RELEASE_3_23). Checks:1 ERROR, 2 WARNING, 1 OK. Indexed: no.

This is a data package. Data packages may be large and do not get checked across all platforms.

Target	Result	Time
bioc-checks	ERROR	223
linux-devel	WARNING	354
source / vignettes	OK	547
linux-release	WARNING	354

Exports:align_target align_target_bowtie blast_reassignment convert_animalcules convert_animalcules_patho convert_animalcules_silva count_matches download_accessions download_refseq download_refseq_16S extract_reads filter_host filter_host_bowtie get_children meta_demultiplex metascope_blast metascope_id metascope_inspect metascope_inspect_usage mk_bowtie_index mk_subread_index run_metascope

Dependencies:abind askpass BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocParallel Biostrings bit bit64 bitops blob cachem cli clipr codetools cpp11 crayon curl data.table DBI dbplyr DelayedArray dplyr farver fastmap filelock formatR futile.logger futile.options generics GenomicRanges ggplot2 glue gtable hms httr2 IRanges isoband labeling lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats memoise MultiAssayExperiment openssl pillar pkgconfig prettyunits progress purrr R.methodsS3 R.oo R.utils R6 Rbowtie2 RColorBrewer readr Rhtslib rlang Rsamtools RSQLite S4Arrays S4Vectors S7 scales Seqinfo snow SparseArray stringi stringr SummarizedExperiment sys taxonomizr tibble tidyr tidyselect tzdb utf8 vctrs viridisLite vroom withr XVector

Introduction to MetaScope

Rendered fromMetaScope_vignette.Rmdusingknitr::rmarkdown

Last update: 2025-04-06
Started: 2022-03-10

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
A universal parameter settings object for Rsubread alignment	align_details
Align microbiome reads to a set of reference libraries	align_target
Align microbiome reads to set of indexed Bowtie2 libraries	align_target_bowtie
Replace the header from a .bam file	bam_reheader_R
Reassign reads from MetaScope BLASTn alignment	blast_reassignment
Calculates result metrics from a blast results table	blast_result_metrics
Reformat BLASTn results	blastn_results
blastn_single_result	blastn_single_result
A universal parameter object for Bowtie 2 16S alignment	bt2_16S_params
A universal parameter object for Bowtie 2 metagenomic alignment where the host genome is thought to be absent from the reference database	bt2_missing_params
A universal parameter object for Bowtie 2 metagenomic or non-16S alignment	bt2_regular_params
Check if blastn exists on the system	check_blastn_exists
Check if samtools exists on the system	check_samtools_exists
Create a combined .bam header	combined_header
Create a multi-assay experiment from MetaScope output for usage with animalcules	convert_animalcules
Create a multi-assay experiment from PathoScope 2.0 output for usage with animalcules	convert_animalcules_patho
Create a multi-assay experiment from MetaScope output for usage with animalcules with the SILVA 13_8 database	convert_animalcules_silva
Count the number of base lengths in a CIGAR string for a given operation	count_matches
Download indexes required for MetaScope ID and MetaBlast modules	download_accessions
Download RefSeq genome libraries	download_refseq
Download RefSeq 16S rRNA Bacterial and Archael libraries	download_refseq_16S
Helper function for demultiplexing	extract_reads
Use Rsubread to align reads against one or more filter libraries and subsequently remove mapped reads	filter_host
Use Rbowtie2 to align reads against one or more filter libraries and subsequently remove mapped reads	filter_host_bowtie
Filter unmapped reads	filter_unmapped_reads
Get child nodes from NCBI taxonomy	get_children
Gets sequences from bam file	get_seqs
Helper Function for MetaScope ID	locations
Merge multiple .bam files	merge_bam_files
Demultiplexing sequencing reads	meta_demultiplex
Blast reads from MetaScope aligned files	metascope_blast
Identify which genomes are represented in a processed sample	metascope_id
Inspect a Bowtie index	metascope_inspect
Print available arguments that can be passed to metascope_inspect()	metascope_inspect_usage
Make a Bowtie2 index	mk_bowtie_index
Make a Subread index	mk_subread_index
Helper function to remove reads matched to filter libraries	remove_matches
Converts NCBI taxonomy ID to scientific name	taxid_to_name