sights: Statistics and dIagnostic Graphs for HTS
Version 1.2.0

SIGHTS is a suite of normalization methods, statistical tests, and diagnostic graphical tools for high throughput screening (HTS) assays. HTS assays use microtitre plates to screen large libraries of compounds for their biological, chemical, or biochemical activity.

Browse man pages Browse package API and functions Browse package files

AuthorElika Garg [aut, cre], Carl Murie [aut], Heydar Ensha [ctb], Robert Nadon [aut]
Bioconductor views BatchEffect CellBasedAssays MicrotitrePlateAssay MultipleComparison Normalization Preprocessing QualityControl Visualization
Date of publicationNone
MaintainerElika Garg <elika.garg@mail.mcgill.ca>
LicenseGPL-3 | file LICENSE
Version1.2.0
URL https://eg-r.github.io/sights/
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("sights")

Man pages

ex_dataMatrix: High-Throughput Screening example data - CMBA
inglese: High-Throughput Screening example data - Inglese
normLoess: Normalization by loess method
normMedFil: Normalization by median filter method
normR: Normalization by R score method
normRobZ: Normalization by robust Z score method
normSights: Normalization methods
normSPAWN: Normalization by SPAWN method
normZ: Normalization by Z score method
plot3d: 3D plot
plotAutoco: Auto-correlation
plotBox: Boxplot
plotHeatmap: Heat map
plotHist: Histogram
plotIGFit: Inverse gamma
plotScatter: Scatter plot
plotSights: Graphical devices
statFDR: FDR control
statRVM: RVM Test
statSights: Statistical methods
statT: t-test

Functions

RVT1 Source code
RVT1Sided Source code
applyMedFilter Source code
checkNA Source code
createNeighbourhoodMatrix Source code
createSequentialNeighbourhoodMatrix Source code
ex_dataMatrix Man page
flik Source code
getLen Source code
getab Source code
inglese Man page
loessMe Source code
medMe Source code
myRVM Source code
myRobZ Source code
myT Source code
myZ Source code
myca Source code
normLoess Man page Source code
normMedFil Man page Source code
normR Man page Source code
normRobZ Man page Source code
normSPAWN Man page Source code
normSights Man page Source code
normZ Man page Source code
plot3d Man page Source code
plotAutoco Man page Source code
plotBox Man page Source code
plotHeatmap Man page Source code
plotHist Man page Source code
plotIGFit Man page Source code
plotScatter Man page Source code
plotSights Man page Source code
rlmRConly Source code
rowVars Source code
sightsCheck Source code
spawning Source code
statFDR Man page Source code
statRVM Man page Source code
statSights Man page Source code
statT Man page Source code
trimPolish Source code

Files

DESCRIPTION
LICENSE
NAMESPACE
R
R/ex_dataMatrix.R
R/inglese.R
R/internal.R
R/normLoess.R
R/normMedFil.R
R/normR.R
R/normRobZ.R
R/normSPAWN.R
R/normSights.R
R/normZ.R
R/plot3d.R
R/plotAutoco.R
R/plotBox.R
R/plotHeatmap.R
R/plotHist.R
R/plotIGFit.R
R/plotScatter.R
R/plotSights.R
R/statFDR.R
R/statRVM.R
R/statSights.R
R/statT.R
R/sysdata.rda
build
build/vignette.rds
data
data/ex_dataMatrix.rda
data/inglese.rda
inst
inst/CITATION
inst/NEWS
inst/NEWS.md
inst/doc
inst/doc/sights.R
inst/doc/sights.Rmd
inst/doc/sights.html
man
man/ex_dataMatrix.Rd
man/inglese.Rd
man/normLoess.Rd
man/normMedFil.Rd
man/normR.Rd
man/normRobZ.Rd
man/normSPAWN.Rd
man/normSights.Rd
man/normZ.Rd
man/plot3d.Rd
man/plotAutoco.Rd
man/plotBox.Rd
man/plotHeatmap.Rd
man/plotHist.Rd
man/plotIGFit.Rd
man/plotScatter.Rd
man/plotSights.Rd
man/statFDR.Rd
man/statRVM.Rd
man/statSights.Rd
man/statT.Rd
tests
tests/testthat
tests/testthat.R
tests/testthat/inglese.rda
tests/testthat/inglese_results.rda
tests/testthat/test_Invalid.R
tests/testthat/test_Loess.R
tests/testthat/test_MedFilter.R
tests/testthat/test_Plot.R
tests/testthat/test_R.R
tests/testthat/test_RobZ.R
tests/testthat/test_SPAWN.R
tests/testthat/test_Stat.R
tests/testthat/test_Z.R
vignettes
vignettes/Usi29DB.tmp
vignettes/bibliography.bib
vignettes/bioinformatics.csl
vignettes/sights.Rmd
sights documentation built on May 20, 2017, 9:31 p.m.