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 Source code
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
acm.burt Man page
acm.disjonctif Man page
addHighlightLegend2 Source code
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 Source code
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
betaABfromMeanKappa Source code
betaABfromMeanSD Source code
betaABfromModeKappa 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
calinhara 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.p.values Source code Source code
combine.test Man page Source code Source code
compute.absCN Man page Source code
constructMotifs3 Source code
context3d Source code
core_sig Source code
cosine Source code 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
fastICA.v2 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
gammaShRaFromMeanSD Source code
gammaShRaFromModeSD 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
isvaFn.v2 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
motifMatrix Source code
mshapiro.test Man page Source code
mut_cor_permu_test Man page Source code
mutationContext 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 Source code
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
plotgenome 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 Source code
sample_with_replace Source code Source code
saveGraph Source code
scale01 Source code
scale02 Source code
scatterutil.base Source code
scatterutil.ellipse Source code
scatterutil.eti Source code
scatterutil.grid Source code
scatterutil.star Source code
scatterutil.sub 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
lixiangchun/lxctk documentation built on May 21, 2017, 1:40 p.m.