Package: coRdon 1.25.0
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:
coRdon_1.25.0.tar.gz
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coRdon.pdf |coRdon.html✨
coRdon/json (API)
NEWS
| # 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
- 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-1.25.0(bioc 3.21)coRdon-1.24.0(bioc 3.20)
softwaremetagenomicsgeneexpressiongenesetenrichmentgenepredictionvisualizationkeggpathwaysgenetics cellbiologybiomedicalinformaticsimmunooncology
Last updated 2 months agofrom:c2f3cd04f8. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 29 2024 |
| R-4.5-win | OK | Nov 29 2024 |
| R-4.5-linux | OK | Nov 29 2024 |
| R-4.4-win | OK | Nov 29 2024 |
| R-4.4-mac | OK | Nov 29 2024 |
| R-4.3-win | OK | Nov 29 2024 |
| R-4.3-mac | OK | Nov 29 2024 |
Exports:BBplotCAIcodonCountscodonTablecontablecrossTabEENCENCprimeenrichBarplotenrichMAplotenrichMatrixenrichmentFopGCBgetCOGgetIDgetKOgetlengetSeqAnnotgetVariableintraBplotMCBMELPMILCreadSetreduceCrossTabSCUOsetCOGsetKOshow
Dependencies:askpassBiobaseBiocGenericsBiostringsclicolorspacecrayoncurldata.tabledplyrfansifarvergenericsGenomeInfoDbGenomeInfoDbDataggplot2gluegtablehttrIRangesisobandjsonlitelabelinglatticelifecyclemagrittrMASSMatrixmgcvmimemunsellnlmeopensslpillarpkgconfigpurrrR6RColorBrewerrlangS4VectorsscalesstringistringrsystibbletidyselectUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc
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 |
