MetaScope

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17

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

Bioconductor version: Development (3.24)

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: Sean Lu [aut, cre] ORCID: 0009-0007-8005-6125 , Aubrey Odom [aut] ORCID: 0000-0001-7113-7598 , Rahul Varki [aut] ORCID: 0009-0003-5721-9484 , W. Evan Johnson [aut] ORCID: 0000-0002-6247-6595

Maintainer: Sean Lu <seanlu96 at gmail.com>

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

Sean Lu, Aubrey Odom, Rahul Varki, W. Evan Johnson. MetaScope: Tools and functions for preprocessing 16S and metagenomic sequencing microbiome data. doi:10.18129/B9.bioc.MetaScope, R package version 2.1.0, https://bioconductor.org/packages/MetaScope.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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")

"Introduction to MetaScope"	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ExperimentData, MicrobiomeData, ReproducibleResearch, SequencingData
Version	2.1.0
In Bioconductor since	BioC 3.17 (R-4.3) (3.5 years)
License	GPL (>= 3)
Depends	R (>= 4.2.0)
Imports	BiocFileCache, Biostrings, data.table (>= 1.16.2), dplyr, ggplot2, magrittr, Matrix, MultiAssayExperiment, purrr, Rbowtie2, readr, rlang, Rsamtools, S4Vectors, stringr, SummarizedExperiment, taxonomizr, 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

Suggests	animalcules, BiocStyle, biomformat, GenomicRanges, IRanges, knitr, lintr, plyr, R.utils, RCurl, rmarkdown, Rsubread, spelling, sys, testthat, usethis
Linking To
Enhances	BiocParallel
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	MetaScope_2.1.0.tar.gz
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)
macOS Binary (sonoma-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