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>
citation("MetaScope")):
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")| Introdution to MetaScope | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
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 |
| System Requirements | |
| URL | https://github.com/compbiomed/metascope https://compbiomed.github.io/metascope-docs/ |
| Bug Reports | https://github.com/compbiomed/MetaScope/issues |
See More
| Suggests | BiocStyle, biomformat, knitr, lintr, plyr, 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.
| 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 |