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: Sean Lu [aut, cre]
, Aubrey Odom [aut]
, Rahul Varki [aut]
, W. Evan Johnson [aut]
Maintainer: Sean Lu <seanlu96 at gmail.com>
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")| Introduction to MetaScope | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ExperimentData, MicrobiomeData, ReproducibleResearch, SequencingData |
| Version | 1.9.10 |
| License | GPL (>= 3) |
| Depends | R (>= 4.1.0) |
| 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, RCurl, 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_1.9.10.tar.gz |
| 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 git@git.bioconductor.org:packages/MetaScope |
| Package Short Url | https://bioconductor.org/packages/MetaScope/ |
| Package Downloads Report | Download Stats |