MetaScope

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


Bioconductor version: Release (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 bu.edu>

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

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("MetaScope")

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

Documentation

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

browseVignettes("MetaScope")
Introdution to MetaScope HTML R Script
Introdution to MetaScope HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews ExperimentData, MicrobiomeData, ReproducibleResearch, SequencingData
Version 1.5.4
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
URL https://github.com/wejlab/metascope https://wejlab.github.io/metascope-docs/
Bug Reports https://github.com/wejlab/MetaScope/issues
See More
Suggests animalcules, BiocStyle, biomformat, GenomicRanges, IRanges, knitr, lintr, plyr, R.utils, rmarkdown, Rsubread, spelling, sys, taxonomizr, testthat, usethis
Linking To
Enhances BiocParallel
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Package Archives

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

Source Package MetaScope_1.5.4.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/MetaScope
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MetaScope
Package Short Url https://bioconductor.org/packages/MetaScope/
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