MetaScope
This is the released version of MetaScope; for the devel version, see MetaScope.
Tools and functions for preprocessing 16S and metagenomic sequencing microbiome data
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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")| Introduction to MetaScope | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ExperimentData, MicrobiomeData, ReproducibleResearch, SequencingData |
| Version | 2.0.0 |
| License | GPL (>= 3) |
| 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 |
| 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_2.0.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-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 |