API for lixiangchun/lxctk
Li Xiangchun's tool-kit (lxctk)
| Global functions | |
|---|---|
| Adjust_Sig_Rigions | Source code |
| AlexandrovEtAl_signatures_annotation | Source code |
| AlexandrovEtAl_signatures_corr | Man page Source code |
| BayesNMF.L1KL | Source code |
| BayesNMF.L2KL | Source code |
| BayesNMF.MutationalSignatures | Man page |
| BayesNMF.mutation.signature | Source code |
| BreastCancerRelatedGenes | Man page |
| CIplot | Source code |
| COSMIC_signatures_annotation | Source code |
| COSMIC_signatures_corr | Man page Source code |
| CancerDB | Man page |
| CancerGeneCensus | Man page |
| CancerRelatedGenes | Man page |
| ChromatinRegulatoryGenes | Man page |
| DbdaAcfPlot | Source code |
| DbdaDensPlot | Source code |
| DbdaDensPlot2 | Man page Source code |
| Diagonalize_Regions | Source code |
| DoISVA.v2 | Man page |
| Error_Of_Regions | Source code |
| HDIofGrid | Source code |
| HDIofICDF | Source code |
| HDIofMCMC | Source code |
| HDIofMCMC.stanfit | Man page Source code |
| LandscapeColor | Man page |
| LixcCuratedPathway | Man page |
| MutSigCL | Source code Source code |
| MutSigCLFN | Source code Source code |
| MutSigFN | Source code Source code |
| MutSigXX.Statistic | Source code |
| OncogenicSignatureGeneSet | Man page |
| PathwayDB | Man page |
| RegularMutatedGC | Man page |
| RunMEGSA | Man page Source code |
| Simulate_Regions | Source code |
| Smooth_Regions | Source code |
| TARGET_db | Man page |
| Test_Regions | Source code |
| `fixcolorvector` | Source code |
| `makecombinedname` | Source code |
| `seemslog` | Source code |
| acm.burt | Man page |
| acm.disjonctif | Man page |
| annotate.dbnsfp | Source code Source code Source code |
| annotateVRanges | Source code Source code Source code |
| as.numeric.frame | Source code |
| barplot.image | Source code |
| bayes.student_t | Man page Source code |
| bayes.t.test | Man page Source code |
| beanplot | Man page |
| beanplot2 | Man page |
| best.robust_t_test | Man page Source code |
| best.robust_t_test_batch | Man page Source code |
| best.robust_t_test_model | Source code |
| best.robust_t_test_model2 | Source code |
| best.student_t | Man page Source code |
| best.student_t_model | Source code |
| boxplot.acm | Man page |
| boxplot.jitter | Man page Source code |
| calc_allelic_freqs | Man page Source code |
| calc_allelic_freqs_core | Source code |
| cat.CI | Source code |
| cat.RR | Source code |
| cluster.solution | Source code |
| cmds | Source code |
| cmds.focal.test | Man page Source code |
| cmds.focal.test2 | Source code |
| cmds.test.plot | Source code |
| cmds.v1 | Source code |
| cn.plot | Source code |
| cn.viberate | Source code |
| collapseMutationContext | Source code Source code Source code |
| combine.test | Man page Source code |
| compute.absCN | Man page Source code |
| constructMotifs3 | Source code |
| context3d | Source code |
| core_sig | Source code |
| diag.mcmc | Man page Source code |
| diagMCMC | Source code |
| diagStanFit | Source code |
| dist.JSD | Man page Source code |
| dudi.acm | Man page |
| evaluate.sig | Source code |
| fac2disj | Source code Source code |
| faster.sample | Source code |
| freq.by.subtype | Source code |
| from.stac | Source code |
| funAdd1 | Source code |
| funAdd1RealData | Source code |
| funDrop1RealData | Source code |
| funEstimate | Source code |
| funGlobalTest | Source code |
| funGradient | Source code |
| funLogLikelihood | Source code |
| funMEGSA | Source code |
| funMaxS | Source code |
| funMaxSSimu | Source code |
| funPlotMEGS | Source code |
| funPlotMutationMat | Source code |
| funPrintMEGS | Source code |
| funSelect | Source code |
| generate_mutsigcl_global_bkgr_info | Source code |
| get.bkgr.dbnsfp | Source code Source code |
| get.df.solution | Source code |
| get.gene.spectra | Source code |
| get.lego96.hyper | Source code |
| get.mutland | Man page Source code |
| get.stats.simulation | Source code |
| getBkgrGeneSignature | Source code Source code Source code |
| getBkgrGeneSignature_dev | Source code Source code Source code |
| getGrpId | Source code Source code Source code |
| getHotspotStatistic | Source code Source code Source code |
| getLongestCCDS | Source code Source code Source code |
| getLongestIsoformPerPosNucleotieGRanges | Source code Source code Source code |
| getObsGeneSigature | Source code Source code Source code |
| ggPlotMutationalSignatures | Man page Source code |
| ggboxplot | Man page Source code |
| ggforestplot | Man page Source code |
| glmfit | Man page Source code |
| grid.search.alpha | Source code |
| grid.search.alpha.simple | Source code |
| gvalues.test | Source code |
| gvalues.test.old | Source code |
| heatCN | Source code |
| is.SQLiteConnection | Source code |
| land.image | Source code |
| landplot | Source code |
| landscape.data | Man page Source code |
| legoplot | Man page Source code |
| lm2 | Man page Source code |
| makeVRangesFromMaf | Source code Source code Source code |
| makeVRangesFromOncotator | Source code Source code |
| matrix.sample.v1 | Source code |
| modified.model | Source code |
| mshapiro.test | Man page Source code |
| mut_cor_permu_test | Man page Source code |
| mutsig.gene | Man page Source code |
| mutsig.pathway | Man page Source code |
| mutsigcl | Source code Source code |
| mutsigclOldVersion | Source code |
| mutsigcl_core | Source code Source code Source code |
| mutsigcl_core2 | Source code Source code |
| mutsigcl_global | Man page Source code |
| mutsigcl_global_core | Source code |
| mutsigclfn | Man page Source code |
| mutsigcv.sig.pathway | Man page Source code |
| mutsigfn_core | Source code Source code |
| mutsigfn_core2 | Source code Source code |
| mutsignr | Man page Source code |
| nature12912_260_Smg | Man page |
| normality_test | Source code |
| normalize | Source code |
| oncoprinter | Man page Source code |
| oncoprinter.sort.data.frame | Source code |
| one.gene.permute | Source code |
| openGraph | Source code |
| optimcluster | Man page Source code |
| optimize.alpha | Source code |
| optimize.alpha.simple | Source code |
| original.model | Source code |
| parse_cds_info | Source code Source code Source code |
| pileup_freqs | Man page Source code |
| plot.96.spectra | Man page Source code |
| plot.CoocurExclus | Man page Source code |
| plot.MH | Man page Source code |
| plot.SciClone | Man page |
| plot.absCN | Man page Source code |
| plot.activity.barplot | Source code |
| plot.coocur | Man page Source code |
| plot.coocur2 | Man page Source code |
| plot.coxph | Man page Source code |
| plot.depth | Man page Source code |
| plot.land | Source code |
| plot.landscape2 | Man page Source code |
| plot.lego.observed.barplot | Source code |
| plot.logit | Man page Source code |
| plot.multinom | Man page Source code |
| plot.mutation.signature | Man page Source code |
| plot.mutational.exposures | Man page Source code |
| plot.mutational.processes | Man page Source code |
| plot.spectra | Man page Source code |
| plot.surv.curve | Man page Source code |
| plot.survfit.lixc | Man page Source code |
| plotMutationalProcesses | Man page Source code |
| plotPost | Man page Source code |
| plotroc | Source code |
| prob.concur | Source code |
| rank.based.INT | Man page Source code |
| read.ncbi.ccds.file | Source code Source code |
| run.absCNSeq | Man page Source code |
| run.cn.farms.from.Celfiles | Source code |
| runRF | Man page Source code |
| s.class2 | Man page |
| sample_with_replace | Source code Source code |
| saveGraph | Source code |
| scale01 | Source code |
| scale02 | Source code |
| seq.vjoint | Source code |
| sort.data.frame | Man page Source code Source code Source code |
| sort.data.frame.by.index | Man page Source code |
| sortDataFrame | Man page Source code |
| stackplot.3d | Source code |
| stad_SMGs_vs_MSig | Source code |
| stanfit2mcmc.list | Man page Source code |
| student_t_distribution_model | Source code |
| subtype.image | Source code |
| summarizePost | Source code |
| theme_small_axis | Source code |
| theme_ss | Source code |
| to.stac | Source code |
| unicoxph | Man page Source code |
| vioplot | Man page Source code |
| vioplot2 | Man page Source code |
| which.xy | Man page Source code |
| window.test | Source code |
