occugene: Functions for Multinomial Occupancy Distribution

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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.

Author
Oliver Will <oliverrreader@gmail.com>
Date of publication
None
Maintainer
Oliver Will <oliverrreader@gmail.com>
License
GPL (>= 2)
Version
1.34.0

View on Bioconductor

Man pages

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

Files in this package

occugene/DESCRIPTION
occugene/NAMESPACE
occugene/R
occugene/R/cloneFunc.R
occugene/R/formatManip.R
occugene/R/insertFunc.R
occugene/R/multOccup.R
occugene/build
occugene/build/vignette.rds
occugene/data
occugene/data/sampleAnnotation.txt
occugene/data/sampleInsertions.txt
occugene/inst
occugene/inst/doc
occugene/inst/doc/occugene.R
occugene/inst/doc/occugene.Rnw
occugene/inst/doc/occugene.pdf
occugene/man
occugene/man/binHist.Rd
occugene/man/binInsert.Rd
occugene/man/binInsertHist.Rd
occugene/man/checkFormat.Rd
occugene/man/delta0.Rd
occugene/man/eMult.Rd
occugene/man/etDelta.Rd
occugene/man/fCumul.Rd
occugene/man/fFit.Rd
occugene/man/loadAnnotation.Rd
occugene/man/loadInsertions.Rd
occugene/man/occup2Negenes.Rd
occugene/man/sampleAnnotation.Rd
occugene/man/sampleInsertions.Rd
occugene/man/unbiasB0.Rd
occugene/man/unbiasDelta0.Rd
occugene/man/varMult.Rd
occugene/vignettes
occugene/vignettes/occugene.Rnw
occugene/website_description.txt