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MetaScope

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

Bioconductor version: Release (3.17)

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

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

Maintainer: Aubrey Odom-Mabey <aodom at bu.edu>

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

Installation

To install this package, start R (version "4.3") 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
Reference Manual PDF
NEWS Text

Details

biocViews ExperimentData, MicrobiomeData, ReproducibleResearch, SequencingData
Version 1.0.0
License GPL (>= 3)
Depends R (>= 4.2.0)
Imports BiocFileCache, Biostrings, data.table, dplyr, ggplot2, magrittr, Matrix, MultiAssayExperiment, qlcMatrix, R.utils, Rbowtie2, readr, rlang, Rsamtools, S4Vectors, stringr, SummarizedExperiment, taxize, tidyr, tools
Linking To
Suggests BiocStyle, biomformat, knitr, lintr, plyr, rmarkdown, Rsubread, spelling, sys, testthat, usethis
System Requirements
Enhances BiocParallel
URL https://github.com/compbiomed/metascope https://compbiomed.github.io/metascope-docs/
Bug Reports https://github.com/compbiomed/MetaScope/issues
See More
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package MetaScope_1.0.0.tar.gz
Windows Binary
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/
Package Downloads Report Download Stats