Man pages for lixiangchun/lxctk
Li Xiangchun's tool-kit (lxctk)

AlexandrovEtAl_signatures_corrCalculate cosine similarity of mutational signature with...
BayesNMF.MutationalSignaturesPerform Bayesian NMF mutational signature analysis
bayes.student_tBayesian inference to estimate the parameters of student's t...
bayes.t.testRobust student's t-test based on Bayesian statistics.
beanplotBeanplot: A Boxplot/Stripchart/Vioplot Alternative
beanplot2Beanplot: A Boxplot/Stripchart/Vioplot Alternative
best.robust_t_testRobust student's t-test based on Bayesian statistics.
best.robust_t_test_batchBatch running robust t-test.
best.student_tBayesian inference to estimate the parameters of student's t...
boxplot.jitterboxplot with scatter points
BreastCancerRelatedGenesBreast cancer related genes affected by mutations curated...
calc_allelic_freqsCalculate allelic frequencies.
CancerDBCancer related genes and pathways curated from published...
CancerGeneCensusCancer Gene Census.
CancerRelatedGenesCancer related genes affected by mutations curated from...
ChromatinRegulatoryGenesChromatin regulatory genes implicated in human cancers...
cmds.focal.testCorrelation matrix diagonal segmentation(CMDS) to identify...
combine.testCombine multiple p-values
compute.absCNConvert copy ratios into abosolute copy numbers when given...
COSMIC_signatures_corrCalculate cosine similarity of mutational signature with...
DbdaDensPlot2Density plot of posterior distribution of a given model...
diag.mcmcMCMC diagnostics plot.
dist.JSDJensen-Shannon divergence (JSD) distance.
DoISVA.v2Feature selection using independent surrogate variables...
dudi.acmMultiple Correspondence Analysis
get.mutlandPrepare data for 'plot.landscape'
ggboxplotFancy boxplot via ggplot2
ggforestplotforestplot via ggplot2
ggPlotMutationalSignaturesPlotting mutational signatures
glmfitPlot posterior distribution of a given parameter
HDIofMCMC.stanfitHDI for stanFit object
LandscapeColorMultiple color scheme designed for 'plot.landscape'.
landscape.dataPrepare data for 'plot.landscape'
legoplotLegoplot exihibition of 96 mutational categories.
LixcCuratedPathwayCancer related pathways affected by mutations curated from...
lm2Perform a simple linear regression model
mshapiro.testShapiro-Wilk Multivariate Normality Test. Source code from...
mut_cor_permu_testMuSiC Mutation Relation Analysis
mutsigclfnPermutation-based identification of Significantly Mutated...
mutsigcl_globalPermutation-based identification of hotspot-enriched genes...
mutsigcv.sig.pathwayIdentify significantly mutated pathways based on MutSigCV...
mutsig.geneCanonical algorithms to detect significantly mutated genes
mutsignrMutsig analysis of somatic mutations in noncoding region
mutsig.pathwayCanonical algorithms to detect significantly mutated genes
nature12912_260_Smg260 SMG from nature12912.
OncogenicSignatureGeneSetOncogenic signatures gene sets curated by GSEA.
oncoprinterOncoPrinter - Visualizing mutational landscape of SMGs.
optimclusterOptimal clustering via PAM
PathwayDBCanonical pathways curated by GSEA.
pileup_freqsCreate a table of A,C,G,T nucleotide frequencies for pileup...
plot.96.spectraVisualize mutation spectra in 96 contexts
plot.absCNplot estimated integer copy numbers from absCNseq for each...
plot.coocurVisualize mutation coocurrence and exclusivity.
plot.coocur2Visualize mutation coocurrence and exclusivity.
plot.CoocurExclusVisualize mutation coocurrence and exclusivity.
plot.coxphDraw a forestplot to visualize multivariate Cox regression...
plot.depthVisualize sequencing depth and coverage at different levels
plot.landscape2Visualize mutation landscape
plot.logitVisualize a logit model object.
plot.MHVisualize mountain-hill landscape with package 'rgl'
plot.multinomVisualize a multiple logit model object return by 'multinom'...
plot.mutational.exposuresVisualizing mutational exposures.
plot.mutational.processesPlot mutational processes obtaining from mutational signature...
plotMutationalProcessesPlot mutation signatures.
plot.mutation.signaturePlot mutation signatures.
plotPostPlot posterior distribution of a given parameter
plot.SciCloneplot.SciClone: Plot kernel density and copy number...
plot.spectraVisualize mutation spectra in 6 or 8 contexts
plot.surv.curveSurvival curve visualization with additional information.
plot.survfit.lixcSurvival curve visualization with additional information.
rank.based.INTRank-based Inverse Normal Transformation
RegularMutatedGCSMGs in regular-mutated genes and related clinicopathological...
run.absCNSeqmain function to run absCNseq
RunMEGSARunning Mutually Exclusive Gene Set Analysis.
runRFRun random forest classifier training and visualization
s.class2Plot of factorial maps with representation of point classes...
sort.data.frameSort a data frame by multiple columns or user-specified...
sortDataFrameSort a data frame by multiple columns or user-specified...
sort.data.frame.by.indexSort data frame by columns allowing for different block of...
stanfit2mcmc.listConvert rstan::stanfit object to coda:mcmc.list.
TARGET_dbTARGET_db
unicoxphPerform univariate Cox Regression Analysis for multipe...
vioplotviolin plot
vioplot2violin plot
which.xyGet indexes of a vector or an element in other unique vector.
lixiangchun/lxctk documentation built on May 21, 2017, 1:40 p.m.