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CHANGES IN VERSION 1.14.0
-------------------
NEW FEATURES
o Add function to parse MEME output.
o Add parallel computing of searchSeq.
CHANGES IN VERSION 1.12.0
-------------------
BUG FIXES
o Fix a bug in PFMSimilarity.
o Fix an error when there are multiple classes for motif matrx.
NEW FEATURES
o readJASPARMatrix function to add the JASPAR format file.
CHANGES IN VERSION 1.10.0
-------------------
BUG FIXES
o Adapt the runMEME to work with meme 4.10.x version.
o Fix the scientific notation in run_MEME
o Better error handling of MEME wrappe
CHANGES IN VERSION 1.9.4
------------------------
NEW FEATURES
o Add conversion from IUPAC string to matrix
o toPWM, toICM work on PFMatrixList
BUG FIXES
o Fix the seqLogo error when the frequency of each base is same
at certain site. Thanks to Liz.
o Fix the database interface to deal with the duplicated/missing records
for certain TFBS in JASPAR2016.
o Fix coersion method failure on certain cases.
CHANGES IN VERSION 1.7.2
------------------------
NEW FEATURES
o New class TFFMFirst and TFFMDetail for next generation TFBSs.
o Novel TFFM sequence logo.
BUG FIXES
o Fix the bug in runMEME, which always return positive strand for
site sequence.
CHANGES IN VERSION 1.5.0
------------------------
NEW FEATURES
o searchSeq now works on DNAStringSet.
The names in DNAStringSet will be used as seqname in SiteSet.
o More user-friendly output in data.frame or GRanges from SiteSet,
SiteSetList, et al.
o reverseComplement works on XMatrix now.
o faster implmentation of searchPairBSgenome
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