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:Laurent Gautier

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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'))

Datasets:

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.

annotation visualization

2.30 score 1 scripts 336 downloads 17 exports 3 dependencies

Last updated 2 months agofrom:926c9815df. Checks:ERROR: 1 WARNING: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	FAIL	Dec 22 2024
R-4.5-win	WARNING	Dec 22 2024
R-4.5-linux	WARNING	Dec 22 2024
R-4.4-win	WARNING	Dec 22 2024
R-4.4-mac	WARNING	Dec 22 2024
R-4.3-win	WARNING	Dec 22 2024
R-4.3-mac	WARNING	Dec 22 2024

Exports:arrowsArc chromPos2angle cPlotCircle ecoli.len gccontent linesArc linesChrom linesCircle linkedmultiget pointsArc polar2xy polygonArc polygonChrom polygonDisk rotate wstringapply xy2polar

Dependencies:Biobase BiocGenerics generics

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Citation

Development and contributors

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