NanoStringNorm: Normalize NanoString miRNA and mRNA Data

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

Author
Daryl M. Waggott
Date of publication
2015-11-18 09:31:04
Maintainer
Paul Boutros <Paul.Boutros@oicr.on.ca>
License
GPL-2
Version
1.1.21

View on CRAN

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

Files in this package

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