Files in tushiqi/MAnorm2
Tools for Normalizing and Comparing ChIP-seq Samples
.Rbuildignore
.gitignore
DESCRIPTION
MAnorm2.Rproj
NAMESPACE
R/MAnorm2.R
R/MAnorm2_ops.R
R/VST.R
R/bioCond.R
R/diffTest.R
R/fitMeanVarCurve.R
R/meanVarCurve.R
R/normalize.R
R/robustMeanVarCurve.R
R/show.R
R/util.R
README.md
data/H3K27Ac.rda
dist/MAnorm2_1.0.0.tar.gz
dist/MAnorm2_1.1.0.tar.gz
dist/MAnorm2_1.2.0.tar.gz
dist/MAnorm2_1.2.1.tar.gz
dist/MAnorm2_1.2.2.tar.gz
inst/CITATION
inst/NEWS
man/H3K27Ac.Rd
man/MA.pcc.Rd
man/MAnorm2.Rd
man/MAplot.Rd
man/MAplot.bioCond.Rd
man/MAplot.diffBioCond.Rd
man/aovBioCond.Rd
man/bioCond.Rd
man/checkCountTable.Rd
man/checkIndex.Rd
man/cmbBioCond.Rd
man/diffTest.Rd
man/distBioCond.Rd
man/estParamHyperChIP.Rd
man/estimateD0.Rd
man/estimateD0Robust.Rd
man/estimatePriorDf.Rd
man/estimatePriorDfRobust.Rd
man/estimateSizeFactors.Rd
man/estimateVarRatio.Rd
man/extendMeanVarCurve.Rd
man/fitMeanVarCurve.Rd
man/intervalMeans.Rd
man/intervalVars.Rd
man/inv.trigamma.Rd
man/isSymPosDef.Rd
man/meanVarLocalFit.Rd
man/meanVarParaFit.Rd
man/mean_var_logwinf.Rd
man/mvcID.new.Rd
man/normBioCond.Rd
man/normBioCondBySizeFactors.Rd
man/normCoef.Rd
man/normalize.Rd
man/normalizeBySizeFactors.Rd
man/plot.aovBioCond.Rd
man/plot.matrix.Rd
man/plot.varTestBioCond.Rd
man/plotMVC.Rd
man/plotMeanVarCurve.Rd
man/print.bioCond.Rd
man/print.summaryBioCond.Rd
man/scaleMeanVarCurve.Rd
man/scaleMeanVarCurveRobust.Rd
man/setMeanVarCurve.Rd
man/setPriorDf.Rd
man/setPriorDfRobust.Rd
man/setPriorDfVarRatio.Rd
man/setWeight.Rd
man/summary.bioCond.Rd
man/util.trigamma.Rd
man/varRatio.Rd
man/varTestBioCond.Rd
man/vstBioCond.Rd
utility/code-HyperChIPPaper/HyperChIP_statistical_simulation.r
utility/code-MAnorm2Paper/DESeq2.r
utility/code-MAnorm2Paper/MAnorm2.r
utility/code-MAnorm2Paper/csaw.r
utility/code-MAnorm2Paper/data/GM12891_cmp_GM12892.H3K4me3_hieMA.xls
utility/code-MAnorm2Paper/data/GM12891_cmp_GM12892.H3K4me3_profile_bins.xls
utility/code-MAnorm2Paper/data/NOTES.txt
utility/code-MAnorm2Paper/limmaTrend.r
utility/code-MAnorm2Paper/normalization.r
utility/code-MAnorm2Paper/statistical_simulation.r
utility/code-MAnorm2Paper/voom.r
utility/code-example/example.R
utility/code-test/GM19238_cmp_GM19239.H3K4me3/GM19238_cmp_GM19239.H3K4me3.R
utility/code-test/GM19238_cmp_GM19239.H3K4me3/GM19238_cmp_GM19239.H3K4me3_DiffMAplot.png
utility/code-test/GM19238_cmp_GM19239.H3K4me3/GM19238_cmp_GM19239.H3K4me3_MVC.png
utility/code-test/GM19238_cmp_GM19239.H3K4me3/GM19238_cmp_GM19239.H3K4me3_NormMAplot.png
utility/code-test/GM19238_cmp_GM19239.H3K4me3/GM19238_cmp_GM19239.H3K4me3_diffTest.xls
utility/code-test/data/LCLs_Yoruban.H3K4me3/LCLs_Yoruban.H3K4me3_profile_bins.xls
utility/code-test/data/LCLs_Yoruban.H3K4me3/LCLs_Yoruban.H3K4me3_profile_bins_log.txt
utility/code-test/data/LCLs_Yoruban.H3K4me3/parameters_file
utility/code-test/data/LCLs_Yoruban.H3K4me3/stderr
utility/code-test/data/LCLs_Yoruban.H3K4me3/stdout
utility/data-raw/H3K27Ac/LCLs_Caucasian.H3K27ac_example_profile_bins.xls
utility/data-raw/H3K27Ac/LCLs_Caucasian.H3K27ac_example_profile_bins_log.txt
utility/data-raw/H3K27Ac/parameters_file
utility/data-raw/H3K27Ac/stderr
utility/data-raw/H3K27Ac/stdout
utility/vignette-MAnorm2/MAnorm2_vignette.R
utility/vignette-MAnorm2/MAnorm2_vignette.Rmd
utility/vignette-MAnorm2/MAnorm2_vignette.html
vignettes/MAnorm2_vignette.Rmd
vignettes/library.bib
