NanoStringNorm: Normalize NanoString miRNA and mRNA Data
Version 1.1.21

A set of tools for normalizing, diagnostics and visualization of NanoString nCounter data.

Browse man pages Browse package API and functions Browse package files

AuthorDaryl M. Waggott
Date of publication2015-11-18 09:31:04
MaintainerPaul Boutros <Paul.Boutros@oicr.on.ca>
LicenseGPL-2
Version1.1.21
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("NanoStringNorm")

Man pages

NanoString: An rda file storing NanoString example datasets. Currently,...
NanoString.mRNA: A data.frame consisting of Nanostring Rat RNA expression...
NanoStringNorm: Methods for preprocessing NanoString nCounter data
NanoStringNorm-package: A suite of functions for normalization, visualization and...
norm.comp: norm.comp
nsn: Methods for preprocessing NanoString nCounter data.
other.normalization: other.normalization
Plot.NanoStringNorm: Plot.NanoStringNorm
Plot.NanoStringNorm.gvis: Plot.NanoStringNorm.gvis
read.markup.RCC: read.markup.RCC
read.xls.RCC: read.xls.RCC

Functions

NanoString Man page
NanoString.mRNA Man page
NanoStringNorm Man page Source code
NanoStringNorm-package Man page
Plot.NanoStringNorm Man page Source code
Plot.NanoStringNorm.gvis Man page Source code
background.normalization Source code
check.trait.values Source code
code.count.normalization Source code
get.batch.effects Source code
get.beta.se.and.p Source code
get.gene.summary.stats Source code
get.geo.mean Source code
get.mean.sd.and.cv Source code
get.sample.summary.stats Source code
get.trait.summary.stats Source code
get.ttest.and.foldchange Source code
norm.comp Man page Source code
nsn Man page Source code
other.normalization Man page Source code
other.normalization.quantile Source code
other.normalization.rank.normal Source code
other.normalization.vsn Source code
other.normalization.zscore Source code
output.formatting Source code
predict.concentration Source code
probe.correction.factor.normalization Source code
read.markup.RCC Man page Source code
read.xls.RCC Man page Source code
sample.content.normalization Source code
test Source code

Files

inst
inst/scripts
inst/scripts/create_test_input_output_files.R
inst/extdata
inst/extdata/RCC_files
inst/extdata/RCC_files/RCCCollector1_rat_tcdd.xls
inst/extdata/output
inst/extdata/output/mRNA_TCDD_Gene_Summary.txt
inst/extdata/output/mRNA_TCDD_total.sum_SampleContent_Normalization.txt
inst/extdata/output/mRNA_TCDD_max_Background_Normalization.txt
inst/extdata/output/mRNA_TCDD_geo.mean_Code_Count_Normalization.txt
inst/extdata/output/date_data.txt
inst/extdata/output/mRNA_TCDD_NSN_none.txt
inst/extdata/output/mRNA_TCDD_Predict_Conc.txt
inst/extdata/output/mRNA_TCDD_sum_Code_Count_Normalization.txt
inst/extdata/output/mRNA_TCDD_mean_Background_Normalization.txt
inst/extdata/output/mRNA_TCDD_Check_Traits.txt
inst/extdata/output/mRNA_TCDD_top.mean_SampleContent_Normalization.txt
inst/extdata/output/mRNA_TCDD_quantile_Other_Normalization.txt
inst/extdata/output/mRNA_TCDD_housekeeping.sum_SampleContent_Normalization.txt
inst/extdata/output/mRNA_TCDD_Output_Formatting_roundT_logT.txt
inst/extdata/output/mRNA_TCDD_NSN_random.txt
inst/extdata/output/mRNA_TCDD_Batch_effects.txt
inst/extdata/output/mRNA_TCDD_Sample_Summary.txt
inst/extdata/output/mRNA_TCDD_housekeeping.geo.mean_SampleContent_Normalization.txt
inst/extdata/output/mRNA_TCDD_mean.2sd_Background_Normalization.txt
inst/extdata/output/mRNA_TCDD_NSN_none_matrix.txt
inst/extdata/output/mRNA_TCDD_zscore_Other_Normalization.txt
inst/extdata/output/mRNA_TCDD_top.geo.mean_SampleContent_Normalization.txt
inst/extdata/input
inst/extdata/input/mRNA_TCDD_matrix.txt
inst/extdata/input/mRNA_TCDD.txt
inst/extdata/input/2011-11-01_NanoString_mRNA_TCDD_anno.txt
inst/extdata/input/date_data.txt
inst/extdata/input/mRNA_TCDD_anno.txt
inst/extdata/input/mRNA_TCDD_strain_info.txt
inst/doc
inst/doc/NanoStringNorm_Introduction.pdf
inst/doc/NanoStringNorm_Introduction.R
inst/doc/NanoStringNorm_Introduction.Rnw
inst/unitTests
inst/unitTests/test_background.normalization.R
inst/unitTests/debug_test_probe.correction.factor.R
inst/unitTests/test_other.normalization.R
inst/unitTests/test_sample.summary.R
inst/unitTests/test_batch.effects.R
inst/unitTests/test_sample.content.normalization.R
inst/unitTests/test_code.count.normalization.R
inst/unitTests/test_output.formatting.R
inst/unitTests/test_predict.concentration.R
inst/unitTests/test_check.trait.values.R
inst/unitTests/test_NanoStringNorm.R
tests
tests/NanoStringNorm.unitTests.R
NAMESPACE
NEWS
data
data/NanoString.rda
R
R/get.gene.summary.stats.R
R/check.trait.values.R
R/other.normalization.vsn.R
R/get.beta.se.and.p.R
R/other.normalization.quantile.R
R/get.batch.effects.R
R/other.normalization.rank.normal.R
R/get.ttest.and.foldchange.R
R/other.normalization.zscore.R
R/read.markup.RCC.R
R/predict.concentration.R
R/Plot.NanoStringNorm.R
R/read.xls.RCC.R
R/background.normalization.R
R/unit.testing.NanoStringNorm.R
R/norm.comp.R
R/probe.correction.factor.normalization.R
R/get.trait.summary.stats.R
R/output.formatting.R
R/Plot.NanoStringNorm.gvis.R
R/nsn.R
R/get.sample.summary.stats.R
R/other.normalization.R
R/code.count.normalization.R
R/get.geo.mean.R
R/sample.content.normalization.R
R/get.mean.sd.and.cv.R
R/NanoStringNorm.R
vignettes
vignettes/plot_NSN_gvis_sampleStats_screenshot.png
vignettes/plot_NSN_gvis_geneStats_screenshot.png
vignettes/NanoStringNorm_Introduction.Rnw
vignettes/Rat_Strain_Normalization_Method_Comparison.png
MD5
build
build/vignette.rds
DESCRIPTION
man
man/other.normalization.Rd
man/read.xls.RCC.Rd
man/Plot.NanoStringNorm.Rd
man/Plot.NanoStringNorm.gvis.Rd
man/NanoString.mRNA.Rd
man/read.markup.RCC.Rd
man/NanoString.Rd
man/norm.comp.Rd
man/NanoStringNorm-package.Rd
man/nsn.Rd
man/NanoStringNorm.Rd
NanoStringNorm documentation built on May 19, 2017, 4:47 p.m.