Package: ecolitk 1.79.0
Laurent Gautier
ecolitk: Meta-data and tools for E. coli
Meta-data and tools to work with E. coli. The tools are mostly plotting functions to work with circular genomes. They can used with other genomes/plasmids.
Authors:
ecolitk_1.79.0.tar.gz
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ecolitk.pdf |ecolitk.html✨
ecolitk/json (API)
| # Install 'ecolitk' in R: |
| install.packages('ecolitk', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- ecoli.m52.genome - Escherichia coli data
- ecoli.operon - Escherichia coli data
- ecoligenome.operon - Known operon in E.coli - data.frame
- ecoligenomeBNUM - Environment for 'bnum' identifiers
- ecoligenomeBNUM2ENZYME - Environment for 'bnum' identifiers
- ecoligenomeBNUM2GENBANK - Environment for 'bnum' identifiers
- ecoligenomeBNUM2GENEPRODUCT - Environment for 'bnum' identifiers
- ecoligenomeBNUM2MULTIFUN - Environment
- ecoligenomeBNUM2STRAND - Environment
- ecoligenomeBNUM2SYMBOL - Environment for 'bnum' identifiers
- ecoligenomeCHRLOC - Escherichia coli data
- ecoligenomeMULTIFUN2GO - MultiFun classification
- ecoligenomeSTRAND - Escherichia coli data
- ecoligenomeSYMBOL - Escherichia coli data
- ecoligenomeSYMBOL2AFFY - Escherichia coli data
- ecoligenomeSYMBOL2BNUM - Environment for 'bnum' identifiers
- multiFun - MultiFun classification
On BioConductor:ecolitk-1.79.0(bioc 3.21)ecolitk-1.78.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 22 days agofrom:926c9815df. Checks:ERROR: 1 WARNING: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | FAIL | Oct 31 2024 |
| R-4.5-win | WARNING | Oct 31 2024 |
| R-4.5-linux | WARNING | Oct 31 2024 |
| R-4.4-win | WARNING | Oct 31 2024 |
| R-4.4-mac | WARNING | Oct 31 2024 |
| R-4.3-win | WARNING | Oct 31 2024 |
| R-4.3-mac | WARNING | Oct 31 2024 |
Exports:arrowsArcchromPos2anglecPlotCircleecoli.lengccontentlinesArclinesChromlinesCirclelinkedmultigetpointsArcpolar2xypolygonArcpolygonChrompolygonDiskrotatewstringapplyxy2polar
Dependencies:BiobaseBiocGenerics
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Escherichia coli data | ecoli.len ecoli.m52.genome ecoli.operon ecoligenomeCHRLOC ecoligenomeSTRAND ecoligenomeSYMBOL ecoligenomeSYMBOL2AFFY |
| Known operon in E.coli - data.frame | ecoligenome.operon |
| Environment for 'bnum' identifiers | ecoligenomeBNUM ecoligenomeBNUM2ENZYME ecoligenomeBNUM2GENBANK ecoligenomeBNUM2GENEPRODUCT ecoligenomeBNUM2SYMBOL ecoligenomeSYMBOL2BNUM |
| Environment | ecoligenomeBNUM2MULTIFUN ecoligenomeBNUM2STRAND |
| function to compute gccontent | gccontent |
| A function to look for values across linked environments | linkedmultiget |
| multiFun classification | ecoligenomeMULTIFUN2GO multiFun |
| Functions to plot circular related figures | arrowsArc linesArc linesCircle pointsArc polygonArc polygonDisk |
| Functions to perform polar coordinate related functions | polar2xy rotate xy2polar |
| Functions to plot circular chromosomes informations | chromPos2angle cPlotCircle linesChrom polygonChrom |
| Apply a function on a window sliding on a string | wstringapply |
