NEWS

---

TFBSTools 1.14.0

NEW FEATURES

• Add function to parse MEME output.
• Add parallel computing of searchSeq.

TFBSTools 1.12.0

BUG FIXES

• Fix a bug in PFMSimilarity.
• Fix an error when there are multiple classes for motif matrx.

NEW FEATURES

• readJASPARMatrix function to add the JASPAR format file.

TFBSTools 1.10.0

BUG FIXES

• Adapt the runMEME to work with meme 4.10.x version.
• Fix the scientific notation in run_MEME
• Better error handling of MEME wrappe

TFBSTools 1.9.4

NEW FEATURES

• Add conversion from IUPAC string to matrix
• toPWM, toICM work on PFMatrixList

BUG FIXES

• Fix the seqLogo error when the frequency of each base is same at certain site. Thanks to Liz.
• Fix the database interface to deal with the duplicated/missing records for certain TFBS in JASPAR2016.
• Fix coersion method failure on certain cases.

TFBSTools 1.7.2

NEW FEATURES

• New class TFFMFirst and TFFMDetail for next generation TFBSs.
• Novel TFFM sequence logo.

BUG FIXES

• Fix the bug in runMEME, which always return positive strand for site sequence.

TFBSTools 1.5.0

NEW FEATURES

• searchSeq now works on DNAStringSet. The names in DNAStringSet will be used as seqname in SiteSet.
• More user-friendly output in data.frame or GRanges from SiteSet, SiteSetList, et al.
• reverseComplement works on XMatrix now.
• faster implmentation of searchPairBSgenome