Files in calebclass/NanoTube
An Easy Pipeline for NanoString nCounter Data Analysis
.github/workflows/r.yml
DESCRIPTION
LICENSE
NAMESPACE
NEWS.md
R/NanoTube.R
R/deVolcano.R
R/fgseaPostprocessing.R
R/fgseaPostprocessingXLSX.R
R/fgseaToLEdge.R
R/gm_mean.R
R/groupFGSEA.R
R/groupedGSEAtoStackedReport.R
R/limmaToFGSEA.R
R/makeDiffExprFile.R
R/makeFGSEAmasterTable.R
R/makeNanoStringSetFromEset.R
R/nanostringPCA.R
R/negativeQC.R
R/normalize_housekeeping.R
R/normalize_pos_controls.R
R/nsdiffToFGSEA.R
R/positiveQC.R
R/processNanostringData.R
R/read_cpdb_sourceDBs.R
R/read_cpdb_tab.R
R/read_merge_rcc.R
R/read_rcc.R
R/read_sampleData.R
R/remove_background.R
R/runLimmaAnalysis.R
R/untar_dirs.R
R/unzip_dirs.R
README.md
data/ExamplePathways.rda
data/ExampleResults.rda
inst/CITATION
inst/extdata/GSE117751_RAW/GSM3308226_20160715_5609WV-C.RCC
inst/extdata/GSE117751_RAW/GSM3308227_20170504_6090AA-A2.RCC
inst/extdata/GSE117751_RAW/GSM3308228_20170504_6121PF-A2.RCC
inst/extdata/GSE117751_RAW/GSM3308229_20170504_5993KP-A2.RCC
inst/extdata/GSE117751_RAW/GSM3308230_20170504_6536VE-A2.RCC
inst/extdata/GSE117751_RAW/GSM3308231_20170504_6568NC-A2.RCC
inst/extdata/GSE117751_RAW/GSM3308232_20170504_6612MK-A2.RCC
inst/extdata/GSE117751_RAW/GSM3308233_20170504_6636KS-A2.RCC
inst/extdata/GSE117751_RAW/GSM3308234_20170504_6204CL-A2.RCC
inst/extdata/GSE117751_RAW/GSM3308235_20161006_6779BL-B.RCC
inst/extdata/GSE117751_RAW/GSM3308236_20161006_4988CH-A.RCC
inst/extdata/GSE117751_RAW/GSM3308237_20160329_8017DU-A.RCC
inst/extdata/GSE117751_RAW/GSM3308238_20160715_9154ET-A.RCC
inst/extdata/GSE117751_RAW/GSM3308239_20160715_9164SM-A.RCC
inst/extdata/GSE117751_RAW/GSM3308240_20161006_3947MC-A.RCC
inst/extdata/GSE117751_RAW/GSM3308241_20160629_402ER-A.RCC
inst/extdata/GSE117751_RAW/GSM3308242_20160629_991KH-A.RCC
inst/extdata/GSE117751_RAW/GSM3308243_20160715_440JT-B.RCC
inst/extdata/GSE117751_RAW/GSM3308244_20160629_5092AD-A.RCC
inst/extdata/GSE117751_RAW/GSM3308245_20170504_8037AM-A3.RCC
inst/extdata/GSE117751_RAW/GSM3308246_20170911_3905SW-A.RCC
inst/extdata/GSE117751_RAW/GSM3308247_20160629_4231DK-A.RCC
inst/extdata/GSE117751_RAW/GSM3308248_20160628_6372ML-A.RCC
inst/extdata/GSE117751_RAW/GSM3308249_20170911_5665PB-A.RCC
inst/extdata/GSE117751_RAW/GSM3308250_20170911_9134LH-B.RCC
inst/extdata/GSE117751_RAW/GSM3308251_20160715_6034RN-A.RCC
inst/extdata/GSE117751_RAW/GSM3308252_20161006_9219RD-A.RCC
inst/extdata/GSE117751_RAW/GSM3308253_20161005_2068AP-A.RCC
inst/extdata/GSE117751_RAW/GSM3308254_20170504_5885SL-D2.RCC
inst/extdata/GSE117751_RAW/GSM3308255_20170504_9051LS-A3.RCC
inst/extdata/GSE117751_RAW/GSM3308256_20160628_100KB-A2.RCC
inst/extdata/GSE117751_RAW/GSM3308257_20160628_9149DB-A.RCC
inst/extdata/GSE117751_RAW/GSM3308258_20160628_9147BM-A.RCC
inst/extdata/GSE117751_RAW/GSM3308259_20160628_9148CW-A.RCC
inst/extdata/GSE117751_RAW/GSM3308260_20161005_9281JM-A.RCC
inst/extdata/GSE117751_RAW/GSM3308261_20161005_133BK-A.RCC
inst/extdata/GSE117751_RAW/GSM3308262_20161005_134CD-A.RCC
inst/extdata/GSE117751_RAW/GSM3308263_20170911_9653RA-A.RCC
inst/extdata/GSE117751_RAW/GSM3308264_20170911_9655RK-A.RCC
inst/extdata/GSE117751_RAW/GSM3308265_20170911_9656CW-A.RCC
inst/extdata/GSE117751_RAW/GSM3308266_20170911_9654NL-A.RCC
inst/extdata/GSE117751_RAW/GSM3308267_20170911_9660TM-A.RCC
inst/extdata/GSE117751_design_matrix.csv
inst/extdata/GSE117751_expression_matrix.csv
inst/extdata/GSE117751_sample_data.csv
inst/extdata/GSE117751_sample_data_replicates.csv
inst/extdata/GSE117751_series_matrix.txt
man/ExamplePathways.Rd
man/ExampleResults.Rd
man/NanoTube.Rd
man/deVolcano.Rd
man/fgseaPostprocessing.Rd
man/fgseaPostprocessingXLSX.Rd
man/fgseaToLEdge.Rd
man/gm_mean.Rd
man/groupFGSEA.Rd
man/groupedGSEAtoStackedReport.Rd
man/limmaToFGSEA.Rd
man/makeDiffExprFile.Rd
man/makeFGSEAmasterTable.Rd
man/makeNanoStringSetFromEset.Rd
man/nanostringPCA.Rd
man/negativeQC.Rd
man/normalize_housekeeping.Rd
man/normalize_pos_controls.Rd
man/nsdiffToFGSEA.Rd
man/positiveQC.Rd
man/processNanostringData.Rd
man/read_cpdb_sourceDBs.Rd
man/read_cpdb_tab.Rd
man/read_merge_rcc.Rd
man/read_rcc.Rd
man/read_sampleData.Rd
man/remove_background.Rd
man/runLimmaAnalysis.Rd
man/untar_dirs.Rd
man/unzip_dirs.Rd
tests/testthat.R
tests/testthat/test-gm_mean.R
vignettes/NanoTube.Rmd
vignettes/NanoTube.bib
vignettes/NanoTube.html
