coverageFromBedGraph | read coverage from bedGraph files |
coverageRate | coverage rate of genes and 3UTRs |
covThreshold | calculate the cutoff threshold of coverage |
CPsite_estimation | estimate the cpsites |
CPsites | predict the cleavage and polyadenylation(CP) site |
depthWeight | calculate the depth weight for each example |
distalAdj | adjust distal CP sites by cleanUpdTSeq |
filterRes | filter results |
fisher.exact.test | do fisher exact test for two group datasets |
getCov | extract coverage from bedgraph file |
get.regions.coverage | claculate coverage for giving region |
getUTR3eSet | prepare dataset for test |
getUTR3region | extract long and short 3UTR region |
inPAS | do estimation of alternative polyadenylation and cleavage... |
InPAS-package | alternative polyadenylation and cleavage estimations |
lastCDSusage | extract coverage of last CDS exon region |
limmaAnalyze | use limma to analyze the PDUI |
optimalSegmentation | calculate SSE |
PAscore | calculate the CP score |
PAscore2 | calculate the CP score |
polishCPs | polish the searching results of CP sites |
prepare4GSEA | prepare the files for GSEA analysis |
proximalAdj | adjust the proximal CP sites |
proximalAdjByCleanUpdTSeq | adjust the proximal CP sites by cleanUpdTseq |
proximalAdjByPWM | adjust the proximal CP sites by PWM |
removeUTR3__UTR3 | remove the candicates LIKE UTR3___UTR3 |
searchDistalCPs | search distal CP sites |
searchProximalCPs | search proximal CPsites |
seqLen | get sequence lengths |
singleGroupAnalyze | do analysis for single group samples |
singleSampleAnalyze | do analysis for single sample |
sortGR | sort GRanges |
testUsage | do test for dPDUI |
totalCoverage | total coverage |
trimSeqnames | trim the sequence names |
usage4plot | prepare coverage data and fitting data for plot |
utr3Annotation | extract 3'UTR from TxDb object |
utr3.danRer10 | 3'UTR annotation for danRer10 obtained from utr3Annotation |
UTR3eSet | Class 'UTR3eSet' |
utr3.hg19 | 3'UTR annotation for hg19 obtained from utr3Annotation |
utr3.mm10 | 3'UTR annotation for mm10 obtained from utr3Annotation |
UTR3TotalCoverage | extract coverage of 3UTR for CP sites prediction |
UTR3usage | calculate the usage of long and short form of UTR3 |
utr3UsageEstimation | estimation of 3'UTR usage for each region |
valley | get the local minimal square standard error (SSE) |
zScoreThrethold | calculate local background cutoff value |
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