Registration Open for Bioc2024 July 24-26


This is the development version of MetaScope; for the stable release version, see MetaScope.

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

Bioconductor version: Development (3.20)

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.

Author: Aubrey Odom [aut, cre] , Rahul Varki [aut], W. Evan Johnson [aut] , Howard Fan [ctb]

Maintainer: Aubrey Odom <aodom at>

Citation (from within R, enter citation("MetaScope")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Introdution to MetaScope HTML R Script
Reference Manual PDF


biocViews ExperimentData, MicrobiomeData, ReproducibleResearch, SequencingData
Version 1.5.1
License GPL (>= 3)
Depends R (>= 4.3.0)
Imports BiocFileCache, Biostrings, data.table, dplyr, ggplot2, magrittr, Matrix, MultiAssayExperiment, Rbowtie2, readr, rlang, Rsamtools, S4Vectors, stringr, SummarizedExperiment, taxize, tibble, tidyr, tools
System Requirements
Bug Reports
See More
Suggests animalcules, BiocStyle, biomformat, GenomicRanges, IRanges, knitr, lintr, plyr, rmarkdown, R.utils, Rsubread, spelling, sys, testthat, taxonomizr, usethis
Linking To
Enhances BiocParallel
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package MetaScope_1.5.1.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone
Source Repository (Developer Access) git clone
Package Short Url
Package Downloads Report Download Stats