chem16S

Chemical metrics for microbial communities

https://github.com/jedick/chem16s

Science Score: 67.0%

This score indicates how likely this project is to be science-related based on various indicators:

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
✓
DOI references
Found 14 DOI reference(s) in README
✓
Academic publication links
Links to: ncbi.nlm.nih.gov, zenodo.org
○
Academic email domains
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (11.4%) to scientific vocabulary

Keywords

16s-rrna carbon-oxidation-state chemical-metrics genomic-adaptation microbial-communities r

Last synced: 6 months ago · JSON representation ·

Repository

Chemical metrics for microbial communities

Basic Info

Host: GitHub
Owner: jedick
License: gpl-3.0
Language: R
Default Branch: main
Homepage: https://chnosz.net/chem16S
Size: 13.7 MB

Statistics

Stars: 4
Watchers: 1
Forks: 0
Open Issues: 0
Releases: 7

Topics

16s-rrna carbon-oxidation-state chemical-metrics genomic-adaptation microbial-communities r

Created almost 4 years ago · Last pushed 7 months ago

Metadata Files

Readme License Citation

chem16S generates chemical representations of microbial communities by combining taxonomic abundances of archaea and bacteria with reference sequences for proteins. Chemical metrics for community reference proteomes are used to investigate genomic adaptations to environmental conditions. Potential applications range from human microbiomes to Earth-life coevolution.

Read the paper in Bioinformatics: chem16S: community-level chemical metrics for exploring genomic adaptation to environments.
View the manual and vignettes: Chemical metrics of reference proteomes for taxa, Integration of chem16S with phyloseq, and Plotting two chemical metrics.

Methods

The user provides taxonomic classifications of high-throughput 16S rRNA gene sequences. These are combined with reference proteomes for archaea and bacteria to obtain the amino acid compositions of community reference proteomes. Amino acid compositions used to calculate chemical metrics including carbon oxidation state (Z_C) and stoichiometric hydration state (nH₂O).

Supported input formats: * phyloseq-class objects created using phyloseq * RDP Classifier output

Supported reference databases:

Genome Taxonomy Database (GTDB release 220)
NCBI Reference Sequence Database (RefSeq release 206)
Scripts used to generate reference proteomes for genus- and higher-level archaeal and bacterial taxa (and viruses for RefSeq) are available in the GTDB_220 and RefSeq_206 directories.

Details:

The taxonomic classifier should be trained on 16S rRNA sequences from GTDB so that taxon names are matched to GTDB reference proteomes available in chem16S. Training files are available for DADA2 and the RDP Classifier.
For taxonomic classifications made using the RDP training set (No. 18 07/2020, used in RDP Classifier version 2.13), chem16S includes manual mappings to the NCBI taxonomy described by Dick and Tan (2023).

Example

The Baltic Sea has a salinity gradient from freshwater to marine conditions. Progressively lower nH₂O of community reference proteomes along this gradient represent a genomically coded dehydration trend.

PSU stands for practical salinity units. The sequence data analyzed for this plot was taken from Herlemann et al. (2016) and the code to make this plot is available in the help page for chem16S::plot_metrics.

Installation

First install phyloseq from Bioconductor:

if(!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("phyloseq")

Then install the release version of chem16S from CRAN:

install.packages("chem16S")

Or use install_github from remotes or devtools to install the development version of chem16S from GitHub:

if(!require("remotes", quietly = TRUE)) install.packages("remotes") remotes::install_github("jedick/chem16S", build_vignettes = TRUE)

Owner

Name: Jeffrey Dick
Login: jedick
Kind: user
Location: Changsha, China
Company: Central South University

Website: https://chnosz.net/jeff
Repositories: 4
Profile: https://github.com/jedick

Theoretical geochemist and developer of CHNOSZ.

Citation (CITATION.cff)

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Dick"
  given-names: "Jeffrey M."
  orcid: "https://orcid.org/0000-0002-0687-5890"
title: "chem16S"
doi: 10.5281/zenodo.6793059
url: "https://github.com/jedick/chem16S"
preferred-citation:
  type: article
  authors:
  - family-names: "Dick"
    given-names: "Jeffrey M."
    orcid: "https://orcid.org/0000-0002-0687-5890"
  - family-names: "Kang"
    given-names: "Xun"
  doi: "10.1093/bioinformatics/btad564"
  journal: "Bioinformatics"
  month: 9
  start: btad564
  title: "chem16S: community-level chemical metrics for exploring genomic adaptation to environments"
  issue: 9
  volume: 39
  year: 2023

GitHub Events

Total

Release event: 1
Push event: 13
Create event: 1

Last Year

Release event: 1
Push event: 13
Create event: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time

Total issues: 0
Total pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Total issue authors: 0
Total pull request authors: 0
Average comments per issue: 0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 0
Pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 0
Pull request authors: 0
Average comments per issue: 0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- cran 227 last-month

Total dependent packages: 0
Total dependent repositories: 1
Total versions: 3
Total maintainers: 1

cran.r-project.org: chem16S

Chemical Metrics for Microbial Communities

Homepage: https://github.com/jedick/chem16S
Documentation: http://cran.r-project.org/web/packages/chem16S/chem16S.pdf
License: GPL-3
Latest release: 1.2.0
published about 1 year ago

Versions: 3
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 227 Last month

Rankings

Dependent repos count: 23.8%

Stargazers count: 25.5%

Forks count: 27.8%

Dependent packages count: 28.7%

Average: 37.7%

Downloads: 82.6%

Maintainers (1)

j3ffdick@gmail.com