Package: coRdon 1.31.0

Anamaria Elek

coRdon: Codon Usage Analysis and Prediction of Gene Expressivity

Tool for analysis of codon usage in various unannotated or KEGG/COG annotated DNA sequences. Calculates different measures of CU bias and CU-based predictors of gene expressivity, and performs gene set enrichment analysis for annotated sequences. Implements several methods for visualization of CU and enrichment analysis results.

Authors:Anamaria Elek [cre, aut], Maja Kuzman [aut], Kristian Vlahovicek [aut]

coRdon_1.31.0.tar.gz
coRdon_1.31.0.zip(r-4.7)coRdon_1.31.0.zip(r-4.6)coRdon_1.31.0.zip(r-4.5)
coRdon_1.31.0.tgz(r-4.6-any)coRdon_1.31.0.tgz(r-4.5-any)
coRdon_1.31.0.tar.gz(r-4.7-any)coRdon_1.31.0.tar.gz(r-4.6-any)
coRdon_1.31.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
coRdon/json (API)

# Install 'coRdon' in R:

install.packages('coRdon', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bioinfohr/cordon/issues

Datasets:

HD59 - Codon usage in healthy human gut microbiome.
HD59_KO - Codon usage based KO enrichment analysis results from the healthy human gut microbiome. For more information, see '?HD59'.
HD59_PATHWAYS - Codon usage based KEGG Pathway enrichment analysis results from a healthy human gut microbiome. For more information, see '?HD59'.
LD94 - Codon usage in human gut microbiome in liver cirrhosis.
LD94_KO - Codon usage based KO enrichment analysis results from an gut microbiome of an individual with liver cirrhosis. For more information, see '?LD94'.
LD94_PATHWAYS - Codon usage based KEGG Pathway enrichment analysis results from an gut microbiome of an individual with liver cirrhosis. For more information, see '?LD94'.

On BioConductor:coRdon-1.31.0(bioc 3.24)coRdon-1.30.0(bioc 3.23)

software metagenomics geneexpression genesetenrichment geneprediction visualization kegg pathways genetics cellbiology biomedicalinformatics immunooncology

8.03 score 23 stars 1 packages 86 scripts 6 mentions 32 exports 37 dependencies

Last updated from:86ceb2eb0a. Checks:1 WARNING, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	165
linux-devel-x86_64	OK	264
source / vignettes	OK	235
linux-release-x86_64	OK	241
macos-release-arm64	OK	115
macos-oldrel-arm64	OK	126
windows-devel	OK	176
windows-release	OK	154
windows-oldrel	OK	154
wasm-release	OK	118

Exports:B Bplot CAI codonCounts codonTable contable crossTab E ENC ENCprime enrichBarplot enrichMAplot enrichMatrix enrichment Fop GCB getCOG getID getKO getlen getSeqAnnot getVariable intraBplot MCB MELP MILC readSet reduceCrossTab SCUO setCOG setKO show

Dependencies:Biobase BiocGenerics Biostrings cli cpp11 crayon data.table dplyr farver generics ggplot2 glue gtable IRanges isoband labeling lifecycle magrittr pillar pkgconfig purrr R6 RColorBrewer rlang S4Vectors S7 scales Seqinfo stringi stringr tibble tidyselect utf8 vctrs viridisLite withr XVector

Codon usage (CU) analysis in R

Rendered fromcoRdon.Rmdusingknitr::rmarkdown

Last update: 2018-10-18
Started: 2018-03-26

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Subset 'codonTable' object.	subset.codonTable [,codonTable-method [[,codonTable-method
Karlin B plot	Bplot Bplot,character,character,matrix-method Bplot,numeric,numeric,missing-method
An S4 class 'codonTable'	codonCounts codonCounts,codonTable-method codonTable codonTable,data.frame-method codonTable,DNAStringSet-method codonTable,matrix-method codonTable-class getCOG getCOG,codonTable-method getID getID,codonTable-method getKO getKO,codonTable-method getlen getlen,codonTable-method setCOG setCOG,codonTable-method setKO setKO,codonTable-method
Calculate CU measures.	B B,codonTable-method codonUsage ENC ENC,codonTable-method ENCprime ENCprime,codonTable-method MCB MCB,codonTable-method MILC MILC,codonTable-method SCUO SCUO,codonTable-method
Calculate CU expressivity measures.	CAI CAI,codonTable-method codonUsage-expressivity E E,codonTable-method Fop Fop,codonTable-method GCB GCB,codonTable-method MELP MELP,codonTable-method
coRdon: codon usage analysis in R	coRdon-package coRdon
An S4 class 'crossTab'	contable contable,crossTab-method crossTab crossTab,character,numeric-method crossTab-class getSeqAnnot getSeqAnnot,crossTab-method getVariable getVariable,crossTab-method
Barplot of enriched and depleted annotations.	enrichBarplot enrichBarplot,AnnotatedDataFrame-method enrichBarplot,list-method
MA plot of enriched annotations.	enrichMAplot enrichMAplot,AnnotatedDataFrame-method enrichMAplot,list-method
Extract chosen enrichment values to a matrix.	enrichMatrix enrichMatrix,list-method
Enrichment analysis for codon usage (CU) data.	enrichment enrichment,crossTab-method
An S4 class 'genCode'	genCode genCode,ANY-method genCode-class
Codon usage in healthy human gut microbiome.	HD59
Codon usage based KO enrichment analysis results from the healthy human gut microbiome. For more information, see `?HD59`.	HD59_KO
Codon usage based KEGG Pathway enrichment analysis results from a healthy human gut microbiome. For more information, see `?HD59`.	HD59_PATHWAYS
Intra-samples Karlin B plot	intraBplot intraBplot,codonTable,codonTable-method
Codon usage in human gut microbiome in liver cirrhosis.	LD94
Codon usage based KO enrichment analysis results from an gut microbiome of an individual with liver cirrhosis. For more information, see `?LD94`.	LD94_KO
Codon usage based KEGG Pathway enrichment analysis results from an gut microbiome of an individual with liver cirrhosis. For more information, see `?LD94`.	LD94_PATHWAYS
Length of 'codonTable' object.	length,codonTable-method length-codonTable
Length of 'crossTab' object.	length,crossTab-method length-crossTab
Read set of sequences.	readSet
Reduce 'crossTab'.	reduceCrossTab reduceCrossTab,crossTab,character-method
KEGG Orthology (KO) annotations for ribosomal genes.	RPKOs
Display the object of 'codonTable' class.	show,codonTable-method show-codonTable
Display the object of 'crossTab' class.	show,crossTab-method show-crossTab