Paketti: r-bioc-dada2 (1.32.0+dfsg-1)

[ Source: r-bioc-dada2  ]

sample inference from amplicon sequencing data

The dada2 package contributes to software workflows to interpret sequencing data from microbiota - the relative abundance of bacterial and/or yeast, typically measured in the gut. It infers exact amplicon sequence variants (ASVs) from high-throughput amplicon sequencing data, replacing the coarser and less accurate OTU clustering approach. The dada2 pipeline takes as input demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier, and species-level assignment to 16S rRNA gene fragments by exact matching.

Muut pakettiin r-bioc-dada2 liittyvät paketit

• dep: libc6 (>= 2.38)

  GNU-C-kirjasto: jaetut kirjastot
  myös näennäispaketti, jonka toteuttaa libc6-udeb

• dep: libgcc-s1 (>= 3.0)

  GCC:n apukirjasto

• dep: libstdc++6 (>= 14)

  GNU standardi C++ -kirjasto, versio 3

• dep: libtbb12 (>= 2021.4.0)

  parallelism library for C++ - runtime files

• dep: r-api-4.0

  näennäispaketti, jonka toteuttaa r-base-core

• dep: r-api-bioc-3.19

  näennäispaketti, jonka toteuttaa r-bioc-biocgenerics

• dep: r-bioc-biocgenerics (>= 0.22.0)

  generic functions for Bioconductor

• dep: r-bioc-biostrings (>= 2.42.1)

  GNU R string objects representing biological sequences

• dep: r-bioc-iranges (>= 2.6.0)

  GNU R low-level containers for storing sets of integer ranges

• dep: r-bioc-shortread (>= 1.32.0)

  GNU R classes and methods for high-throughput short-read sequencing data

• dep: r-bioc-xvector (>= 0.16.0)

  BioConductor representation and manpulation of external sequences

• dep: r-cran-ggplot2 (>= 2.1.0)

  implementation of the Grammar of Graphics

• dep: r-cran-rcpp (>= 0.12.0)

  GNU R package for Seamless R and C++ Integration

• dep: r-cran-rcppparallel (>= 4.3.0)

  parallel programming tools for Rcpp

• dep: r-cran-reshape2 (>= 1.4.1)

  Flexibly reshape data: a reboot of the reshape package

• sug: r-bioc-biocstyle

  standard styles for vignettes and other Bioconductor documents

• sug: r-cran-knitr

  GNU R package for dynamic report generation using Literate Programming

• sug: r-cran-rmarkdown

  convert R markdown documents into a variety of formats

Imuroi r-bioc-dada2

Imurointi kaikille saataville arkkitehtuureille

Arkkitehtuuri	Paketin koko	Koko asennettuna	Tiedostot
amd64	2,745.5 kt	3,148.0 kt	[tiedostoluettelo]