MetaScope
Tools and functions for preprocessing 16S and metagenomic sequencing microbiome data
Bioconductor version: Release (3.19)
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] , Rahul Varki [aut], W. Evan Johnson [aut] , Howard Fan [ctb]
Maintainer: Aubrey Odom <aodom at bu.edu>
citation("MetaScope")
):
Installation
To install this package, start R (version "4.4") 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 | 1.4.0 |
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 |
See More
Suggests | animalcules, BiocStyle, biomformat, GenomicRanges, IRanges, knitr, lintr, plyr, qlcMatrix, rBLAST, rmarkdown, R.utils, 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_1.4.0.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 |