MetaScope

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 (3.21)

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] (ORCID: ), Rahul Varki [aut], W. Evan Johnson [aut] (ORCID: ), 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 "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("MetaScope")

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

Documentation


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ExperimentData, MicrobiomeData, ReproducibleResearch, SequencingData
Version	1.7.0
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

Suggests	animalcules, BiocStyle, biomformat, GenomicRanges, IRanges, knitr, lintr, plyr, R.utils, rmarkdown, Rsubread, spelling, sys, taxonomizr, testthat, 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
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 [email protected]:packages/MetaScope
Package Short Url	https://bioconductor.org/packages/MetaScope/
Package Downloads Report	Download Stats