Man pages for lixiangchun/lxctk
Li Xiangchun's tool-kit (lxctk)
| AlexandrovEtAl_signatures_corr | Calculate cosine similarity of mutational signature with... |
| BayesNMF.MutationalSignatures | Perform Bayesian NMF mutational signature analysis |
| bayes.student_t | Bayesian inference to estimate the parameters of student's t... |
| bayes.t.test | Robust student's t-test based on Bayesian statistics. |
| beanplot | Beanplot: A Boxplot/Stripchart/Vioplot Alternative |
| beanplot2 | Beanplot: A Boxplot/Stripchart/Vioplot Alternative |
| best.robust_t_test | Robust student's t-test based on Bayesian statistics. |
| best.robust_t_test_batch | Batch running robust t-test. |
| best.student_t | Bayesian inference to estimate the parameters of student's t... |
| boxplot.jitter | boxplot with scatter points |
| BreastCancerRelatedGenes | Breast cancer related genes affected by mutations curated... |
| calc_allelic_freqs | Calculate allelic frequencies. |
| CancerDB | Cancer related genes and pathways curated from published... |
| CancerGeneCensus | Cancer Gene Census. |
| CancerRelatedGenes | Cancer related genes affected by mutations curated from... |
| ChromatinRegulatoryGenes | Chromatin regulatory genes implicated in human cancers... |
| cmds.focal.test | Correlation matrix diagonal segmentation(CMDS) to identify... |
| combine.test | Combine multiple p-values |
| compute.absCN | Convert copy ratios into abosolute copy numbers when given... |
| COSMIC_signatures_corr | Calculate cosine similarity of mutational signature with... |
| DbdaDensPlot2 | Density plot of posterior distribution of a given model... |
| diag.mcmc | MCMC diagnostics plot. |
| dist.JSD | Jensen-Shannon divergence (JSD) distance. |
| DoISVA.v2 | Feature selection using independent surrogate variables... |
| dudi.acm | Multiple Correspondence Analysis |
| get.mutland | Prepare data for 'plot.landscape' |
| ggboxplot | Fancy boxplot via ggplot2 |
| ggforestplot | forestplot via ggplot2 |
| ggPlotMutationalSignatures | Plotting mutational signatures |
| glmfit | Plot posterior distribution of a given parameter |
| HDIofMCMC.stanfit | HDI for stanFit object |
| LandscapeColor | Multiple color scheme designed for 'plot.landscape'. |
| landscape.data | Prepare data for 'plot.landscape' |
| legoplot | Legoplot exihibition of 96 mutational categories. |
| LixcCuratedPathway | Cancer related pathways affected by mutations curated from... |
| lm2 | Perform a simple linear regression model |
| mshapiro.test | Shapiro-Wilk Multivariate Normality Test. Source code from... |
| mut_cor_permu_test | MuSiC Mutation Relation Analysis |
| mutsigclfn | Permutation-based identification of Significantly Mutated... |
| mutsigcl_global | Permutation-based identification of hotspot-enriched genes... |
| mutsigcv.sig.pathway | Identify significantly mutated pathways based on MutSigCV... |
| mutsig.gene | Canonical algorithms to detect significantly mutated genes |
| mutsignr | Mutsig analysis of somatic mutations in noncoding region |
| mutsig.pathway | Canonical algorithms to detect significantly mutated genes |
| nature12912_260_Smg | 260 SMG from nature12912. |
| OncogenicSignatureGeneSet | Oncogenic signatures gene sets curated by GSEA. |
| oncoprinter | OncoPrinter - Visualizing mutational landscape of SMGs. |
| optimcluster | Optimal clustering via PAM |
| PathwayDB | Canonical pathways curated by GSEA. |
| pileup_freqs | Create a table of A,C,G,T nucleotide frequencies for pileup... |
| plot.96.spectra | Visualize mutation spectra in 96 contexts |
| plot.absCN | plot estimated integer copy numbers from absCNseq for each... |
| plot.coocur | Visualize mutation coocurrence and exclusivity. |
| plot.coocur2 | Visualize mutation coocurrence and exclusivity. |
| plot.CoocurExclus | Visualize mutation coocurrence and exclusivity. |
| plot.coxph | Draw a forestplot to visualize multivariate Cox regression... |
| plot.depth | Visualize sequencing depth and coverage at different levels |
| plot.landscape2 | Visualize mutation landscape |
| plot.logit | Visualize a logit model object. |
| plot.MH | Visualize mountain-hill landscape with package 'rgl' |
| plot.multinom | Visualize a multiple logit model object return by 'multinom'... |
| plot.mutational.exposures | Visualizing mutational exposures. |
| plot.mutational.processes | Plot mutational processes obtaining from mutational signature... |
| plotMutationalProcesses | Plot mutation signatures. |
| plot.mutation.signature | Plot mutation signatures. |
| plotPost | Plot posterior distribution of a given parameter |
| plot.SciClone | plot.SciClone: Plot kernel density and copy number... |
| plot.spectra | Visualize mutation spectra in 6 or 8 contexts |
| plot.surv.curve | Survival curve visualization with additional information. |
| plot.survfit.lixc | Survival curve visualization with additional information. |
| rank.based.INT | Rank-based Inverse Normal Transformation |
| RegularMutatedGC | SMGs in regular-mutated genes and related clinicopathological... |
| run.absCNSeq | main function to run absCNseq |
| RunMEGSA | Running Mutually Exclusive Gene Set Analysis. |
| runRF | Run random forest classifier training and visualization |
| s.class2 | Plot of factorial maps with representation of point classes... |
| sort.data.frame | Sort a data frame by multiple columns or user-specified... |
| sortDataFrame | Sort a data frame by multiple columns or user-specified... |
| sort.data.frame.by.index | Sort data frame by columns allowing for different block of... |
| stanfit2mcmc.list | Convert rstan::stanfit object to coda:mcmc.list. |
| TARGET_db | TARGET_db |
| unicoxph | Perform univariate Cox Regression Analysis for multipe... |
| vioplot | violin plot |
| vioplot2 | violin plot |
| which.xy | Get indexes of a vector or an element in other unique vector. |
