Man pages for cma2015/PEA
An integrated R toolkit for plant epitranscriptome analysis.

classifierBuilding machine learning-based classification models
CMRAnnotationCRM Annotation
CMRCallingIdentify CMRs (chemical modifications of RNA) from...
cross_validationCross validation method
extractCovExtract the reads coverage from BAM file
extractSeqsExtract sequences according to samples
featureEncodingFeature encoding
findConfidentPosSamplesFind confident positive samples
findUnlabelSamplesFind unlabeleded samples
G2TConvert the genomic position to transcriptomic position
getUTRGet the genomic features for each transcript
motifDetectDe novo motif discovery in the peak regions
motifScanScanning the motifs in the peak regions
peakCallingPeak Calling
plotROCPlotting receiver operating characteristic(ROC) Curves
predCMRPredicting the CMR status using machine learning-based models
pseudoURatioPseudouridine ratio
PSOLMachine learning-based PSOL(positive samples only learning...
QCBAMQuality control for BAM format files
readMappingReads mapping
runTopGOGo enrichment
sampleDataexample data for PEA
searchMotifPosScanning the motif in the sequence
SlidingWindowFisher exact test based sliding window
cma2015/PEA documentation built on Dec. 3, 2018, 9:16 p.m.