Anaquin: Statistical analysis of sequins
Version 1.2.0

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.

Browse man pages Browse package API and functions Browse package files

AuthorTed Wong
Bioconductor views DifferentialExpression GeneExpression Preprocessing RNASeq Software
Date of publicationNone
MaintainerTed Wong <t.wong@garvan.org.au>
LicenseBSD_3_clause + file LICENSE
Version1.2.0
URL www.sequin.xyz
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("Anaquin")

Man pages

analysis: Return type of analysis
AnaquinData: Create Anaquin dataset
input: Return input concentration
label: Return classified labels
measured: Return measured abundance
plotLinear: Plot linear model for sequins
plotLODR: Create Limit-of-Detection Ratio (LODR) plot
plotLogistic: Plot logistic model for sequins
plotMA: Create MA plot
plotROC: Create ROC plot
pval: Return p-value probability
qval: Return q-value probability
ratio: Return ratio
RnaQuin.aggregate: Aggregate isoform concentration
RnaQuin.genes: Filter RnaQuin genes
RnaQuin.iso2gen: Convert RnaQuin isoforms to genes
RnaQuin.isoforms: Filter RnaQuin isoforms
RnaQuinMixtureA: RnaQuin mixture A
RnaQuinMixtureB: RnaQuin mixture B
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)

Functions

AnaquinData Man page Source code
RnaQuin.aggregate Man page Man page Source code
RnaQuin.genes Man page Man page Source code
RnaQuin.iso2gen Man page Man page Source code
RnaQuin.isoforms Man page Man page Source code
RnaQuinMixtureA Man page
RnaQuinMixtureB Man page
UserGuideData_5.4.5.1 Man page
UserGuideData_5.4.6.3 Man page
UserGuideData_5.6.3 Man page
analysis Man page
analysis,AnaquinData-method Man page
estimateLOQ Source code
fitCurve Source code
fitLODR Source code
getLODR Source code
input Man page
input,AnaquinData-method Man page
label Man page
label,AnaquinData-method Man page
lm2str Source code
m2str Source code
measured Man page
measured,AnaquinData-method Man page
plotLODR Man page Source code Source code
plotLinear Man page Source code
plotLogistic Man page Source code
plotMA Man page Source code
plotROC Man page Source code
pval Man page
pval,AnaquinData-method Man page
qval Man page
qval,AnaquinData-method Man page
ratio Man page
ratio,AnaquinData-method Man page
score Man page
score,AnaquinData-method Man page
seqs Man page
seqs,AnaquinData-method Man page
std Man page
std,AnaquinData-method Man page
transformPlot Source code
validate Source code
verifyLabel Source code

Files

DESCRIPTION
LICENSE
NAMESPACE
R
R/LOQ.R
R/RnaQuin.R
R/anaquin.R
R/graphics.R
R/plotLODR.R
R/plotLinear.R
R/plotLogistic.R
R/plotMA.R
R/plotROC.R
README.md
build
build/vignette.rds
data
data/RnaQuinMixtureA.rda
data/RnaQuinMixtureB.rda
data/UserGuideData_5.4.5.1.rda
data/UserGuideData_5.4.6.3.rda
data/UserGuideData_5.6.3.rda
inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/Anaquin.R
inst/doc/Anaquin.Rmd
inst/doc/Anaquin.pdf
man
man/AnaquinData.Rd
man/RnaQuin.aggregate.Rd
man/RnaQuin.genes.Rd
man/RnaQuin.iso2gen.Rd
man/RnaQuin.isoforms.Rd
man/RnaQuinMixtureA.Rd
man/RnaQuinMixtureB.Rd
man/UserGuideData_5.4.5.1.Rd
man/UserGuideData_5.4.6.3.Rd
man/UserGuideData_5.6.3.Rd
man/analysis.Rd
man/input.Rd
man/label.Rd
man/measured.Rd
man/plotLODR.Rd
man/plotLinear.Rd
man/plotLogistic.Rd
man/plotMA.Rd
man/plotROC.Rd
man/pval.Rd
man/qval.Rd
man/ratio.Rd
man/score.Rd
man/seqs.Rd
man/std.Rd
tests
tests/tAnaquin.R
tests/tPlotLODR.R
tests/tPlotLinear.R
tests/tPlotLogistic.R
tests/tPlotMA.R
tests/tPlotROC.R
tests/tRnaQuin.R
vignettes
vignettes/Anaquin.Rmd
vignettes/Figure1.png
Anaquin documentation built on May 20, 2017, 9:34 p.m.