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MUSiCC specifications

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Unique identifier OMICS_07839
Name MUSiCC
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data MUSiCC takes as input a raw gene abundance file.
Output data MUSiCC returns a normalized and corrected gene abundance file.
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained No

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Information


Unique identifier OMICS_07839
Name MUSiCC
Interface Web user interface
Restrictions to use None
Input data MUSiCC takes as input a raw gene abundance file.
Output data MUSiCC returns a normalized and corrected gene abundance file.
Programming languages Python
Computer skills Basic
Stability Stable
Maintained No

Maintainer


This tool is not available anymore.

Publication for MUSiCC

MUSiCC citations

 (15)
library_books

The Skin Microbiome of the Neotropical Frog Craugastor fitzingeri: Inferring Potential Bacterial Host Pathogen Interactions From Metagenomic Data

2018
Front Microbiol
PMCID: 5869913
PMID: 29615997
DOI: 10.3389/fmicb.2018.00466

[…] s, the read count was evenly distributed among the corresponding KOs. For example, if a read mapped equally well to 3 KOs, each KO received 1/3 of the count. We normalized the abundances of KOs using MUSiCC (Manor and Borenstein, ) with the inter-sample correction option, which corrects for biases in quantification using the abundance of universal single-copy KOs. […]

call_split

Taxa function robustness in microbial communities

2018
Microbiome
PMCID: 5833107
PMID: 29499759
DOI: 10.1186/s40168-018-0425-4
call_split See protocol

[…] es to first normalize each OTU’s relative abundance by its 16S rRNA copy number and then infer KO abundance from the genomic content of each OTU. KO abundances were then normalized using inter-sample MUSiCC. Pathway-level functional summaries, as defined by the KEGG BRITE hierarchy [], were obtained by evenly distributing each KO’s average copy number across all pathways that contain that KO. Both […]

library_books

Multi omics differentially classify disease state and treatment outcome in pediatric Crohn’s disease

2018
Microbiome
PMCID: 5769311
PMID: 29335008
DOI: 10.1186/s40168-018-0398-3

[…] ng bowtie2 in local alignment mode with MetaPhlAn2 resulted in many spurious hits, which were mainly represented by viruses. These taxa were not identified when global alignment was performed. We ran MUSiCC [] (v1.0.2) to normalize the KO abundances within each sample by the median universal single-copy gene abundance, which controls for inter-sample variation in microbial genome sizes. We then ra […]

library_books

Naked mole rat mortality rates defy Gompertzian laws by not increasing with age

2018
eLife
PMCID: 5783610
PMID: 29364116
DOI: 10.7554/eLife.31157.017

[…] d garnet yams) and supplemented with a high protein and vitamin enriched cereal (Pronutro, South Africa).At 90 days of age, individual mole-rats were sexed, weighed and microchipped, using 12 mm Avid MUSICC microchips, and thereby assigned a unique 9-digit identifier. The microchips were implanted just underneath the dorsal skin in non-anesthetized animals. Thereafter, all animals were weighed reg […]

library_books

Space type radiation induces multimodal responses in the mouse gut microbiome and metabolome

2017
Microbiome
PMCID: 5563039
PMID: 28821301
DOI: 10.1186/s40168-017-0325-z

[…] ts and phylotype-level contributions to functional shifts were obtained using the FishTaco framework []. Input for FishTaco included a pre-computed OTU-KO table from the PICRUSt analysis, output from MUSICC, and OTU relative abundances. FishTaco was run on multi-taxa mode for each pairwise comparison between irradiated and non-irradiated samples. For each KEGG pathway, we estimated both positive a […]

library_books

Proteobacteria explain significant functional variability in the human gut microbiome

2017
Microbiome
PMCID: 5363007
PMID: 28330508
DOI: 10.1186/s40168-017-0244-z

[…] n abundance of a set of 29 bacterial single-copy marker gene families []. These gene families were filtered in the same phylum-specific way as all other gene families. This approach is similar to the MUSiCC method for average genome size correction [] and also controls for overall changes in phylum abundance. We also corrected for AFL as above.Finally, we estimated the average level of overdispers […]


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MUSiCC institution(s)
Department of Genome Sciences, University of Washington, Seattle, WA, USA

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