Pakket: r-bioc-dada2 (1.30.0+dfsg-1 en anderen)

[ Bron: 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.

Andere aan r-bioc-dada2 gerelateerde pakketten

• dep: libc6 (>= 2.34)

  GNU C Bibliotheek: Gedeelde bibliotheken
  Ook een virtueel pakket geboden door: libc6-udeb

• dep: libgcc-s1 (>= 3.0)

  GCC support bibliotheek

• dep: libstdc++6 (>= 11) [x32]

  GNU Standard C++ Library v3

  dep: libstdc++6 (>= 13.1) [amd64]

• dep: libtbb12 (>= 2021.4.0) [amd64]

  parallelism library for C++ - runtime files

• dep: r-api-4.0

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• dep: r-api-bioc-3.16 [x32]

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• dep: r-api-bioc-3.18 [amd64]

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• dep: r-base-core (>= 4.2.2.20221110-1) [x32]

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• 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)

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• dep: r-cran-rcppparallel (>= 4.3.0)

  parallel programming tools for Rcpp

• dep: r-cran-reshape2 (>= 1.4.1)

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• sug: r-bioc-biocstyle

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• sug: r-cran-knitr

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• sug: r-cran-rmarkdown

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r-bioc-dada2 downloaden

Pakket downloaden voor alle beschikbare platforms

Platform	Versie	Pakketgrootte	Geïnstalleerde grootte	Bestanden
amd64	1.30.0+dfsg-1	2.738,8 kB	3.126,0 kB	[overzicht]
x32 (unofficial port)	1.26.0+dfsg-1	2.721,0 kB	3.079,0 kB	[overzicht]