NanoStringNorm: Normalize NanoString miRNA and mRNA Data

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

AuthorDaryl M. Waggott
Date of publication2015-11-18 09:31:04
MaintainerPaul Boutros <Paul.Boutros@oicr.on.ca>
LicenseGPL-2
Version1.1.21

View on CRAN

Files

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

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