MetaScope

DOI: 10.18129/B9.bioc.MetaScope  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see MetaScope.

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

Bioconductor version: 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>

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")

 

HTML	R Script	Introdution to MetaScope
PDF		Reference Manual
Text		NEWS

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
LinkingTo
Suggests	BiocStyle, biomformat, knitr, lintr, plyr, rmarkdown, Rsubread, spelling, sys, testthat, usethis
SystemRequirements
Enhances	BiocParallel
URL	https://github.com/compbiomed/metascope https://compbiomed.github.io/metascope-docs/
BugReports	https://github.com/compbiomed/MetaScope/issues
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