Package: occugene 1.67.0
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:
occugene_1.67.0.tar.gz
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occugene.pdf |occugene.html✨
occugene/json (API)
| # Install 'occugene' in R: |
| install.packages('occugene', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- sampleAnnotation - Annotation for a Hypothetical Prokayote
- sampleInsertions - Insertions for a Hypothetical Clonal Library
On BioConductor:occugene-1.67.0(bioc 3.21)occugene-1.66.0(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 4 months agofrom:c94c038d07. Checks:1 OK, 7 NOTE. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Jan 28 2025 |
| R-4.5-win | NOTE | Jan 28 2025 |
| R-4.5-mac | NOTE | Jan 28 2025 |
| R-4.5-linux | NOTE | Jan 28 2025 |
| R-4.4-win | NOTE | Jan 28 2025 |
| R-4.4-mac | NOTE | Jan 28 2025 |
| R-4.3-win | NOTE | Jan 28 2025 |
| R-4.3-mac | NOTE | Jan 28 2025 |
Exports:checkFormatdelta0eMultetDeltafCumulfFitoccup2NegenesunbiasB0unbiasDelta0varMult
Dependencies:
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 |