diff --git a/DESCRIPTION b/DESCRIPTION index 1f31989..75f658e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ -Date: 2023-09-18 +Date: 2023-09-22 Package: chem16S -Version: 1.0.0-6 +Version: 1.0.0-7 Title: Chemical Metrics of Community Reference Proteomes Authors@R: c( person("Jeffrey", "Dick", , "j3ffdick@gmail.com", role = c("aut", "cre"), diff --git a/README.md b/README.md index 0e28937..15790dc 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,5 @@ -[![CRAN](https://www.r-pkg.org/badges/version/chem16S)](https://cran.r-project.org/package=chem16S) +[![CRAN](https://img.shields.io/badge/dynamic/yaml?url=https%3A%2F%2Fcran.r-project.org%2Fweb%2Fpackages%2Fchem16S%2FDESCRIPTION&query=%24.Version&logo=r&label=CRAN&color=4bc51e)](https://cran.r-project.org/package=chem16S) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.6793059.svg)](https://doi.org/10.5281/zenodo.6793059) [![R-CMD-check](https://github.com/jedick/chem16S/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/jedick/chem16S/actions/workflows/R-CMD-check.yaml) @@ -19,7 +19,7 @@ Supported reference databases: * [Genome Taxonomy Database](https://gtdb.ecogenomic.org/) (GTDB release 207) * [NCBI Reference Sequence Database](https://www.ncbi.nlm.nih.gov/refseq/) (RefSeq release 206) -The *chem16S* R package combines taxonomic classifications of high-throughput 16S rRNA gene sequences with precomputed amino acid compositions of reference proteomes for archaea and bacteria to generate the amino acid compositions of **community reference proteomes**. +The *chem16S* R package combines taxonomic classifications of high-throughput 16S rRNA gene sequences with precomputed amino acid compositions of reference proteomes for archaea and bacteria to obtain the amino acid compositions of **community reference proteomes**. Chemical metrics of community reference proteomes such as **carbon oxidation state** (*Z*C) and **stoichiometric hydration state** (*n*H2O) reveal new ways that microbial genomes are adapted to environmental conditions. For instance, an association of lower *n*H2O with higher salinity in the Baltic Sea suggests a genomically encoded dehydration trend: @@ -33,7 +33,7 @@ The sequence data analyzed for this plot was taken from [Herlemann et al. (2016) ### Methods -* Scripts in the [GTDB](inst/extdata/GTDB) and [RefSeq](inst/extdata/RefSeq) directories were used to generate the reference proteomes for genus- and higher-level archaeal and bacterial taxa (and viruses for RefSeq). +* Scripts in the [GTDB](inst/extdata/GTDB) and [RefSeq](inst/extdata/RefSeq) directories were used to generate reference proteomes for genus- and higher-level archaeal and bacterial taxa (and viruses for RefSeq). * It is recommended to use a GTDB training set for taxonomic classification (e.g. [*DADA2 formatted 16S rRNA gene sequences for both bacteria & archaea*](https://doi.org/10.5281/zenodo.6655692)) so that taxonomic assignments can be automatically matched to GTDB reference proteomes available in *chem16S*. diff --git a/man/chem16S-package.Rd b/man/chem16S-package.Rd index 5b7e5c4..c746810 100644 --- a/man/chem16S-package.Rd +++ b/man/chem16S-package.Rd @@ -168,7 +168,7 @@ Bowen De León K, Gerlach R, Peyton BM, Fields MW. 2013. Archaeal and bacterial Callahan B. 2020. DADA2 Pipeline Tutorial (1.16). \url{https://benjjneb.github.io/dada2/tutorial.html}, accessed on 2023-06-14. -Dick JM, Meng D. 2023. Community- and genome-based evidence for a shaping influence of redox potential on bacterial protein evolution. \emph{mSystems}. \doi{10.1128/msystems.00014-23} +Dick JM, Meng D. 2023. Community- and genome-based evidence for a shaping influence of redox potential on bacterial protein evolution. \emph{mSystems} \bold{8}(3): e00014-23. \doi{10.1128/msystems.00014-23} Dick JM, Tan J. 2023. Chemical links between redox conditions and estimated community proteomes from 16S rRNA and reference protein sequences. \emph{Microbial Ecology} \bold{85}: 1338--1355. \doi{10.1007/s00248-022-01988-9} diff --git a/man/map_taxa.Rd b/man/map_taxa.Rd index 04c7360..0b8a1ba 100644 --- a/man/map_taxa.Rd +++ b/man/map_taxa.Rd @@ -26,7 +26,7 @@ Only exactly matching names are automatically mapped. For mapping to the NCBI (RefSeq) taxonomy, some group names are manually mapped as follows (see Dick and Tan, 2023): \tabular{ll}{ - \strong{Input (i.e., RDP)} \tab \strong{RefSeq} \cr + \strong{RDP training set} \tab \strong{NCBI} \cr genus_Escherichia/Shigella \tab genus_Escherichia \cr phylum_Cyanobacteria/Chloroplast \tab phylum_Cyanobacteria \cr genus_Marinimicrobia_genera_incertae_sedis \tab species_Candidatus Marinimicrobia bacterium \cr