\name{IntEREstnews}
\title{IntEREst News}
\encoding{UTF-8}

\section{CHANGES IN VERSION 1.6.0}{

	\subsection{NEW FEATURES}{

		\itemize{

			\item \code{buildSsTypePwms()} function supports the possibility 
			to select begin and end point of splice sites sequences from which
			PWMs are built. It also supports the possibility to paste splice 
			sites to build PWM.

	

		}
	}

	\subsection{BUG FIXES}{

		\itemize{

		\item \code{interest.sequential()} and \code{interest()} corrections
		to their object output option.

		\item \code{annotateU12()} modified to work correctly with the new 
		changes in \code{Biostrings} package.

		\item \code{buildSsTypePwms()} corrected and modified to better suit 
		data for all species from SpliceRack and U12DB.

		}
	}
}

\section{CHANGES IN VERSION 1.4.0}{

	\subsection{NEW FEATURES}{

		\itemize{

			\item \code{interest()} and \code{interest.sequential()} functions 
			now support \code{"IntSpan"} method, allows counting intron-
			spanning reads.

			\item \code{psi()} function is added. It calculates Psi values.

			\item \code{annotateU12()} fucntion supports DNAStringSet objects 
			as its \code{refGenome} input.

			\item Improved vignette document.


		}
	}

	\subsection{SIGNIFICANT USER-VISIBLE CHANGES}{

		\itemize{

			\item \code{eBayesInterest()} removed.

		}
	}

	\subsection{BUG FIXES}{

		\itemize{

		\item \code{interest.sequential()} and \code{interest()} corrections
		to their object output option.

		\item \code{annotateU12()} modified to work correctly with the new 
		changes in \code{Biostrings} package.

		}
	}
}




