MetaScope

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

Bioconductor version: 3.23 · Package version: 2.0.0

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.

Installation

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

BiocManager::install("MetaScope")

Details

Maintainer	Sean Lu <seanlu96@gmail.com>
Author	Sean Lu [aut, cre] (ORCID: <https://orcid.org/0009-0007-8005-6125>), Aubrey Odom [aut] (ORCID: <https://orcid.org/0000-0001-7113-7598>), Rahul Varki [aut] (ORCID: <https://orcid.org/0009-0003-5721-9484>), W. Evan Johnson [aut] (ORCID: <https://orcid.org/0000-0002-6247-6595>)
License	GPL (>= 3)
URL	https://github.com/wejlab/metascope https://wejlab.github.io/metascope-docs/
Bug Reports	https://github.com/wejlab/MetaScope/issues
Downloads rank	113
Source branch	RELEASE_3_23
biocViews	ExperimentData, MicrobiomeData, ReproducibleResearch, SequencingData

Download

Source package

Dependencies

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

Suggests: animalcules, BiocStyle, biomformat, GenomicRanges, IRanges, knitr, lintr, plyr, R.utils, RCurl, rmarkdown, Rsubread, spelling, sys, testthat, usethis

Enhances: BiocParallel