Anaquin: Statistical analysis of sequins

The project is intended to support the use of sequins (synthetic sequencing spike-in controls) owned and made available by the Garvan Institute of Medical Research. The goal is to provide a standard open source library for quantitative analysis, modelling and visualization of spike-in controls.

Author
Ted Wong
Date of publication
None
Maintainer
Ted Wong <t.wong@garvan.org.au>
License
BSD_3_clause + file LICENSE
Version
1.0.0
URLs

View on Bioconductor

Man pages

analysis
Return type of analysis
AnaquinData
Create Anaquin dataset
input
Return input concentration
label
Return classified labels
measured
Return measured abundance
mixtureA
RnaQuin mixture A
mixtureB
RnaQuin mixture B
mixtureF
RnaQuin mixture F
plotLinear
Plot linear model for sequins
plotLODR
Create Limit-of-Detection Ratio (LODR) plot
plotLogistic
Plot logistic model for sequins
plotROC
Create ROC plot
pval
Return p-value probability
qval
Return q-value probability
ratio
Return ratio
RnaQuin.gen2iso
Convert sequin isoforms to genes
RnaQuin.genes
Return RnaQuin genes
RnaQuin.isoforms
Return RnaQuin isoforms
score
Return scores
seqs
Return sequin names
std
Return standard deviation
UserGuideData_5.4.5.1
Section 5.4.5.1 Assembly Dataset
UserGuideData_5.4.6.3
Gene expression (RnaQuin)
UserGuideData_5.6.3
Differential expression (RnaQuin)

Files in this package

Anaquin/DESCRIPTION
Anaquin/LICENSE
Anaquin/NAMESPACE
Anaquin/R
Anaquin/R/LOQ.R
Anaquin/R/RnaQuin.R
Anaquin/R/anaquin.R
Anaquin/R/graphics.R
Anaquin/R/plotLODR.R
Anaquin/R/plotLinear.R
Anaquin/R/plotLogistic.R
Anaquin/R/plotROC.R
Anaquin/README.md
Anaquin/build
Anaquin/build/vignette.rds
Anaquin/data
Anaquin/data/UserGuideData_5.4.5.1.rda
Anaquin/data/UserGuideData_5.4.6.3.rda
Anaquin/data/UserGuideData_5.6.3.rda
Anaquin/data/mixtureA.rda
Anaquin/data/mixtureB.rda
Anaquin/data/mixtureF.rda
Anaquin/inst
Anaquin/inst/CITATION
Anaquin/inst/NEWS
Anaquin/inst/doc
Anaquin/inst/doc/Anaquin.R
Anaquin/inst/doc/Anaquin.Rmd
Anaquin/inst/doc/Anaquin.pdf
Anaquin/man
Anaquin/man/AnaquinData.Rd
Anaquin/man/RnaQuin.gen2iso.Rd
Anaquin/man/RnaQuin.genes.Rd
Anaquin/man/RnaQuin.isoforms.Rd
Anaquin/man/UserGuideData_5.4.5.1.Rd
Anaquin/man/UserGuideData_5.4.6.3.Rd
Anaquin/man/UserGuideData_5.6.3.Rd
Anaquin/man/analysis.Rd
Anaquin/man/input.Rd
Anaquin/man/label.Rd
Anaquin/man/measured.Rd
Anaquin/man/mixtureA.Rd
Anaquin/man/mixtureB.Rd
Anaquin/man/mixtureF.Rd
Anaquin/man/plotLODR.Rd
Anaquin/man/plotLinear.Rd
Anaquin/man/plotLogistic.Rd
Anaquin/man/plotROC.Rd
Anaquin/man/pval.Rd
Anaquin/man/qval.Rd
Anaquin/man/ratio.Rd
Anaquin/man/score.Rd
Anaquin/man/seqs.Rd
Anaquin/man/std.Rd
Anaquin/tests
Anaquin/tests/tAnaquin.R
Anaquin/tests/tPlotLODR.R
Anaquin/tests/tPlotLinear.R
Anaquin/tests/tPlotLogistic.R
Anaquin/tests/tPlotROC.R
Anaquin/tests/tRnaQuin.R
Anaquin/vignettes
Anaquin/vignettes/Anaquin.Rmd