MetaScope
This is thereleased version of MetaScope; for the devel version, seeMetaScope.
Tools and functions for preprocessing 16S and metagenomic sequencing microbiome data
Bioconductor version: Release (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]
ORCID: 0009-0007-8005-6125, Aubrey Odom [aut] ORCID: 0000-0001-7113-7598, Rahul Varki [aut] ORCID: 0009-0003-5721-9484, W. Evan Johnson [aut] ORCID: 0000-0002-6247-6595
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")BiocManager::install("MetaScope")For older versions of R, please refer to the appropriateBioconductor 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 | 1.10.0 |
| 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/metascopehttps://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
FollowInstallation instructions to use this package in your R session.
| Source Package | MetaScope_1.10.0.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 |