Package: occugene 1.73.0

Oliver Will

occugene: Functions for Multinomial Occupancy Distribution

Statistical tools for building random mutagenesis libraries for prokaryotes. The package has functions for handling the occupancy distribution for a multinomial and for estimating the number of essential genes in random transposon mutagenesis libraries.

Authors:Oliver Will <[email protected]>

occugene_1.73.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
occugene/json (API)

# Install 'occugene' in R:

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

Datasets:

sampleAnnotation - Annotation for a Hypothetical Prokayote
sampleInsertions - Insertions for a Hypothetical Clonal Library

On BioConductor:occugene-1.73.0(bioc 3.24)occugene-1.72.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

annotation pathways

3.30 score 2 scripts 410 downloads 10 exports 0 dependencies

Last updated from:07cdca33f0. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	142
linux-devel-x86_64	NOTE	163
source / vignettes	OK	137
linux-release-x86_64	NOTE	199
macos-release-arm64	NOTE	79
macos-oldrel-arm64	NOTE	64
windows-devel	NOTE	65
windows-release	NOTE	61
windows-oldrel	NOTE	63
wasm-release	OK	81

Exports:checkFormat delta0 eMult etDelta fCumul fFit occup2Negenes unbiasB0 unbiasDelta0 varMult

Dependencies:

occugene

Rendered fromoccugene.Rnwusingutils::Sweave

Last update: 2013-11-01
Started: 2013-11-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Histogram Breakpoints	binHist
Insert Locations	binInsert
Insert Locations Quickly	binInsertHist
Checks the Format of Annotation and Insertions	checkFormat
Number of New Knockouts	delta0
Expected Value of the Occupancy Distribution	eMult
Number of New ORF Knockouts	etDelta
Parametric Function for the Cumulative Occupancy Distribution	fCumul
Parametric Fit for the Cumulative Occupancy Distribution	fFit
Loads Annotation File	loadAnnotation
Load Genome Annotation File	loadInsertions
Convert Occupancy Format to Negenes	occup2Negenes
Annotation for a Hypothetical Prokayote	sampleAnnotation
Insertions for a Hypothetical Clonal Library	sampleInsertions
Unbiased Estimator of the Number of Non-essential ORFs	unbiasB0
Unbiased Number of New Knockouts	unbiasDelta0
Variance of the Occupancy Distribution	varMult