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Showing content from https://bioconductor.org/packages/devel/bioc/html/../../data/experiment/html/MetaScope.html below:

Bioconductor - MetaScope (development version)

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 (3.22)

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

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

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

browseVignettes("MetaScope")
Details biocViews ExperimentData, MicrobiomeData, ReproducibleResearch, SequencingData Version 1.9.3 License GPL (>= 3) Depends R (>= 4.4.0) Imports BiocFileCache, Biostrings, data.table (>= 1.16.2), dplyr, ggplot2, magrittr, Matrix, MultiAssayExperiment, 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 See More Suggests animalcules, BiocStyle, biomformat, GenomicRanges, IRanges, knitr, lintr, plyr, R.utils, rmarkdown, Rsubread, spelling, sys, 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.

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