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ShotgunFunctionalizeR specifications

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Unique identifier OMICS_02623
Name ShotgunFunctionalizeR
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Version 1.2-9
Stability Stable
Requirements
multtest
Maintained Yes

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No version available

Publication for ShotgunFunctionalizeR

ShotgunFunctionalizeR citations

 (17)
library_books

Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics

2016
Front Microbiol
PMCID: 4837688
PMID: 27148170
DOI: 10.3389/fmicb.2016.00459

[…] the functional attributes in shotgun metagenomics data, including mg-rast (meyer et al., ), megan (mitra et al., ), img/m (markowitz et al., ), humann (abubucker et al., ), and the r package shotgunfunctionalizer (kristiansson et al., ). using software like megan5, each sequence can be directly mapped to ko representative sequences and the sum of ko counts that belongs […]

library_books

Gastric microbiota and predicted gene functions are altered after subtotal gastrectomy in patients with gastric cancer

2016
Sci Rep
PMCID: 4748256
PMID: 26860194
DOI: 10.1038/srep20701

[…] to identify gene functions that differentiated bacterial communities before and after surgery, cog gene abundance was subjected to enrichment analysis of two-group comparison, using the r package shotgunfunctionalizer. this analysis normalized gene abundances using a generalized linear model with poisson canonical logarithmic link function and determined differential significance (p-value) […]

library_books

Statistical evaluation of methods for identification of differentially abundant genes in comparative metagenomics

2016
BMC Genomics
PMCID: 4727335
PMID: 26810311
DOI: 10.1186/s12864-016-2386-y

[…] the metagenomic samples []. another early metagenome analysis tool was img/m which performs a test of the relative gene abundances using a gaussian approximation under the null hypothesis [, ]. shotgunfunctionalizer is a software package for r containing several methods but has a focus on regression type approaches using generalized linear models []. metastats is based on a t-test […]

library_books

Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes

2015
PLoS Comput Biol
PMCID: 4643905
PMID: 26565399
DOI: 10.1371/journal.pcbi.1004573

[…] open-source software that completely automates the annotation procedure. most currently available stand-alone tools instead serve as add-ons to the core annotation procedure (e.g., humann, shotgunfunctionalizer []) or limit analyses to specific annotation parameters, such as the reference databases used to contextualize annotations (e.g., megan, rammcap, smashcommunity). […]

library_books

Prokaryotic assemblages and metagenomes in pelagic zones of the South China Sea

2015
BMC Genomics
PMCID: 4373125
PMID: 25879764
DOI: 10.1186/s12864-015-1434-3

[…] groups (cogs) system. only cog assignments with enough significance (e-value ≤10−5) and alignment quality (bit-score ≥100) were involved in the functional enrichment analysis using the r package shotgunfunctionalizer []. the cog gene family frequency was quantified using the number of reads mapped to orfs. every metagenome was compared with all the others (direct comparison of two groups; […]

library_books

An introduction to the analysis of shotgun metagenomic data

2014
Front Plant Sci
PMCID: 4059276
PMID: 24982662
DOI: 10.3389/fpls.2014.00209

[…] to produce pathway coverage and abundance profiles. there are also post-processing tools that analyze protein family classification results produced independently by the researcher. for example, shotgunfunctionalizer () is an r package that enables comparative metagenomic analyses including the identification of families and pathways that are overrepresented in particular samples […]


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ShotgunFunctionalizeR institution(s)
Department of Computer Science And Engineering, Chalmers University of Technology and University of Gothenburg, Göteborg, Sweden

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