Files in lixiangchun/lxctk
Li Xiangchun's tool-kit (lxctk)
DESCRIPTION
NAMESPACE
R/.Rapp.history
R/.Rhistory
R/AlexandrovEtAl_signatures_corr.R
R/BayesNMF.signature_discovery.R
R/COSMIC_signatures_corr.R
R/DBDA2E-utilities.R
R/DbdaDensPlot2.R
R/DoISVA.v2.R
R/MutationRelation.pm.R
R/RunMEGSA.R
R/absCNSeq.R
R/bayes.student_t.R
R/bayes.t.test.R
R/bayes.t.test.model.R
R/beanplot.R
R/beanplot2.R
R/beanplotbeanlines.R
R/beanplotinnerborders.R
R/beanplotpolyshapes.R
R/beanplotscatters.R
R/best.model_codes.R
R/best.model_functions.R
R/best.robust_t_test_batch.R
R/boxplot.jitter.R
R/calc_allelic_freqs.R
R/cmds_lib.R
R/combine.test.R
R/diag.mcmc.R
R/dist.JSD.R
R/dudi.acm.R
R/fixcolorvector.R
R/get.mutland.R
R/getgroupsfromarguments.R
R/ggPlotMutationalSignatures.R
R/ggboxplot.R
R/ggforestplot.R
R/glmfit.R
R/landscape.data.R
R/legoplot.R
R/lm2.R
R/makecombinedname.R
R/mshapiro.test.R
R/mutsig.gene.R
R/mutsig.pathway.R
R/mutsigcl-v1.0.R
R/mutsigcl.R
R/mutsigcl2.R
R/mutsigcl_global.R
R/mutsigclfn.R
R/mutsigcv.sig.pathway.R
R/mutsignr.R
R/oncoprinter.R
R/optimcluster.R
R/pileup_freqs.R
R/plot.96.spectra.R
R/plot.CoocurExclus.R
R/plot.MH.R
R/plot.SciClone.R
R/plot.coocur.R
R/plot.coocur2.R
R/plot.coxph.R
R/plot.depth.R
R/plot.land.R
R/plot.landscape2.R
R/plot.logit.R
R/plot.multinom.R
R/plot.mutation.signature.R
R/plot.mutational.exposures.R
R/plot.mutational.processes.R
R/plot.spectra.R
R/plot.surv.curve.R
R/plot.survfit.lixc.R
R/plotMutationalProcesses.R
R/rank.based.INT.R
R/run.cn.farms.from.Celfiles.R
R/runRF.R
R/s.class2.R
R/seemslog.R
R/sortDataFrame.R
R/unicoxph.R
R/vioplot.R
R/vioplot2.R
R/which.xy.R
README.md
data/AlexandrovEtAl_signatures.RData
data/BreastCancerRelatedGenes.RData
data/BreastCancerRelatedGenes.txt
data/CGC20140319.RData
data/COSMIC_signatures.RData
data/CRCMutMat.RData
data/CancerDB.RData
data/CancerGeneCensus.RData
data/CancerRelatedGenes.RData
data/CanonicalCancerPathway.RData
data/ChromatinRegulatoryGenes.RData
data/LandscapeColor.RData
data/LixcCuratedPathway.RData
data/MH.RData
data/OncogenicSignatureGeneSet.RData
data/PathwayDB.RData
data/Rank_eq_9.exposures.txt
data/Rank_eq_9.processes.txt
data/RegularMutatedGC.RData
data/SLC12A7_tumor_expression.RData
data/SMG.RData
data/TARGET_db.RData
data/TwoGroupIQ.RData
data/absCNseq.RData
data/bayes.t.test.model.RData
data/bayes.t.test.model.txt
data/ccds.depth.RData
data/cds_start_3k_upstream.RData
data/cmds.RData
data/contexts.txt
data/crcdat.RData
data/ggboxplot_data.RData
data/icgc.hcc.RData
data/muSpec.RData
data/nature12912_260_Smg.RData
data/plot.coocur2.test.RData
data/plot.coxph.RData
data/plot.mutation.signature.ex.RData
data/refgene.RData
data/runRF.RData
data/simdataISVA.RData
data/spectra.96.RData
data/stad_regular_GC_originalGenomes.txt
data/x.RData
man/.Rapp.history
man/:q
man/AlexandrovEtAl_signatures_corr.Rd
man/BayesNMF.MutationalSignatures.Rd
man/BreastCancerRelatedGenes.Rd
man/COSMIC_signatures_corr.Rd
man/CancerDB.Rd
man/CancerGeneCensus.Rd
man/CancerRelatedGenes.Rd
man/ChromatinRegulatoryGenes.Rd
man/DbdaDensPlot2.Rd
man/DoISVA.v2.Rd
man/HDIofMCMC.stanfit.Rd
man/LandscapeColor.Rd
man/LixcCuratedPathway.Rd
man/OncogenicSignatureGeneSet.Rd
man/PathwayDB.Rd
man/RegularMutatedGC.Rd
man/RunMEGSA.Rd
man/TARGET_db.Rd
man/bayes.student_t.Rd
man/bayes.t.test.Rd
man/beanplot.Rd
man/beanplot2.Rd
man/best.robust_t_test.Rd
man/best.robust_t_test_batch.Rd
man/best.student_t.Rd
man/boxplot.jitter.Rd
man/calc_allelic_freqs.Rd
man/cmds.focal.test.Rd
man/combine.test.Rd
man/compute.absCN.Rd
man/diag.mcmc.Rd
man/dist.JSD.Rd
man/dudi.acm.Rd
man/get.mutland.Rd
man/ggPlotMutationalSignatures.Rd
man/ggboxplot.Rd
man/ggforestplot.Rd
man/glmfit.Rd
man/landscape.data.Rd
man/legoplot.Rd
man/lm2.Rd
man/mshapiro.test.Rd
man/mut_cor_permu_test.Rd
man/mutsig.gene.Rd
man/mutsig.pathway.Rd
man/mutsigcl_global.Rd
man/mutsigclfn.Rd
man/mutsigcv.sig.pathway.Rd
man/mutsignr.Rd
man/nature12912_260_Smg.Rd
man/oncoprinter.Rd
man/optimcluster.Rd
man/pileup_freqs.Rd
man/plot.96.spectra.Rd
man/plot.CoocurExclus.Rd
man/plot.MH.Rd
man/plot.SciClone.Rd
man/plot.absCN.Rd
man/plot.coocur.Rd
man/plot.coocur2.Rd
man/plot.coxph.Rd
man/plot.depth.Rd
man/plot.landscape2.Rd
man/plot.logit.Rd
man/plot.multinom.Rd
man/plot.mutation.signature.Rd
man/plot.mutational.exposures.Rd
man/plot.mutational.processes.Rd
man/plot.spectra.Rd
man/plot.surv.curve.Rd
man/plot.survfit.lixc.Rd
man/plotMutationalProcesses.Rd
man/plotPost.Rd
man/rank.based.INT.Rd
man/run.absCNSeq.Rd
man/runRF.Rd
man/s.class2.Rd
man/sort.data.frame.Rd
man/sort.data.frame.by.index.Rd
man/sortDataFrame.Rd
man/stanfit2mcmc.list.Rd
man/unicoxph.Rd
man/vioplot.Rd
man/vioplot2.Rd
man/which.xy.Rd
