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