Identification of Transcriptional Dynamics using Pulse Models via 4su-Seq Data and RNA-Seq Data

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Documentation for package ‘pulseTD’ version 0.1.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

correctionParams	Correct the parameters of the pulse model
estimateExpression	Estimated Expression
estimateParams	Estimated pulse model parameters!
getParams	Get pulseModel params
getParams-method	getParams-method
getRates	Get rate values
getRates-method	getRates-method
integrateA	integral function
integrateAC	integral function
plotRates	draw Method
plotRates-method	plotRate-Method
predictExpression	predict Expression
predictExpression-method	predictExpression-method
preExp	A gene list that stores predicted values of gene expression and a 0.95 confidence interval.
pulseModel	pulse function
pulseRates	A pulseTDModel Rdata file containing 100 gene expression data, transcriptional dynamic data already related parameters.
pulseTDmodel	pulseTD-model
pulseTDmodel-class	pulseTD-model
rpkmres	a list containing the expression values of exons and introns
rpkmSim	A simulated gene expressing Rdata file that contains expression data for total RNA, precursor RNA, and 4sU-labeled RNA.
splitA6Params	esitmate transcription parameters
splitB4Params	esitmate degradation parameters
splitC5Params	esitmate processing parameters