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CHNOSZ specifications

Information


Unique identifier OMICS_25824
Name CHNOSZ
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.1.3
Stability Stable
Source code URL https://cran.r-project.org/web/packages/CHNOSZ/index.html
Maintained Yes

Versioning


No version available

Documentation


Maintainers


  • person_outline Jeffrey Dick
  • person_outline Jeffrey Dick

Additional information


http://r-forge.r-project.org/projects/chnosz/

Publication for CHNOSZ

CHNOSZ citations

 (10)
library_books

Influence of Phosphorus and Cell Geometry on the Fractionation of Sulfur Isotopes by Several Species of Desulfovibrio during Microbial Sulfate Reduction

2017
Front Microbiol
PMCID: 5447228
PMID: 28611734
DOI: 10.3389/fmicb.2017.00890

[…] for a hypothetical ideal-dilute solution with unit activity of solutes at concentrations of 10−7 m for h+ and 1 m for all other aqueous species., standard gibbs energies were calculated using the chnosz software package (dick, ) from thermodynamic data (shock and helgeson, ; shock, ; amend and plyasunov, ; wagner and pruß, ; dalla-betta and schulte, ) compiled in database updates […]

library_books

Chemical composition and the potential for proteomic transformation in cancer, hypoxia, and hyperosmotic stress

2017
PeerJ
PMCID: 5463988
PMID: 28603672
DOI: 10.7717/peerj.3421

[…] not contained in the reference proteome were downloaded from uniprot or the ncbi website (for one study reporting gi numbers; see ). amino acid compositions were computed using functions in the chnosz package () or the protparam tool on the uniprot website. the amino acid compositions are stored in *.rdata files in ., r () and r packages canprot (this study) and chnosz () were used […]

library_books

Proteomic indicators of oxidation and hydration state in colorectal cancer

2016
PeerJ
PMCID: 4958012
PMID: 27547546
DOI: 10.7717/peerj.2238

[…] the maier–kelley heat capacity function (, ). properties of liquid h2o were calculated using data and extrapolations coded in fortran subroutines from the supcrt92 package (, ), as provided in the chnosz package (, )., chemical affinities of reactions were calculated using activities of amino acids in the basis equal to 10−4, and activities of proteins equal to 1/(protein length) (i.e., unit […]

library_books

Integrating microbial and host transcriptomics to characterize asthma associated microbial communities

2015
BMC Med Genomics
PMCID: 4537781
PMID: 26277095
DOI: 10.1186/s12920-015-0121-1

[…] microbial communities in each patient., exploratory analysis and differential species abundance testing were performed in r 3.1.2 and bioconductor 3.0 [, ] using packages xlsx 0.5.7, gtools 3.4.1, chnosz 1.0.3.1, plyr 1.8.1, ggplot2 1.0.0, reshape2 1.4.1, gplots 2.16.0, phyloseq 1.10.0, and deseq2 1.6.3 [–]. briefly, various indices (observed, chao1, shannon, simpson) were obtained using […]

library_books

Energy landscapes shape microbial communities in hydrothermal systems on the Arctic Mid Ocean Ridge

2015
PMCID: 4478700
PMID: 25575309
DOI: 10.1038/ismej.2014.247

[…] acid–base reactions were allowed to reach equilibrium. the gwb analyses used the thermo.com thermodynamic database modified to relevant temperatures and pressures using the subcrt command in rs chnosz package (). subcrt calculates the standard molal thermodynamic properties of species and reactions as a function of temperature and pressure, and is modelled after the functionality […]

library_books

Composition, taxonomy and functional diversity of the oropharynx microbiome in individuals with schizophrenia and controls

2015
PeerJ
PMCID: 4556144
PMID: 26336637
DOI: 10.7717/peerj.1140

[…] accurate read counts for downstream analysis., exploratory and differential species abundance analyses were performed in r 3.1.2 and bioconductor 3.0 () using packages xlsx 0.5.7, gtools 3.4.1, chnosz 1.0.3.1, plyr 1.8.1, ggplot2 1.0.0, reshape2 1.4.1, gplots 2.16.0, phyloseq 1.10.0, and deseq2 1.6.3 (; ; ). briefly, various indices (richness: observed, chao1, ace; richness and evenness: […]


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CHNOSZ institution(s)
Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
CHNOSZ funding source(s)
Supported by grants EAR0309829 from the U.S. National Science Foundation and DE-FG02-03ER15418 from the U.S. Department of Energy.

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