CHANGES IN VERSION 1.0.12
-------------------------

BUG FIXES

    o motif_pvalue() no longer throws an error for
      motif_pvalue(..., pvalue = 0)

    o motif_tree() now works properly with dist objects as input

CHANGES IN VERSION 1.0.11
-------------------------

BUG FIXES

    o The compare_motifs() example for min.mean.ic in the Advanced Usage
      vignette now makes more sense

CHANGES IN VERSION 1.0.10
-------------------------

BUG FIXES

    o More strangely behaving MotifDb vignette code addressed in Advanced Usage
      vignette

CHANGES IN VERSION 1.0.9
------------------------

BUG FIXES

    o shuffle_motifs() now produces motifs of proper length

CHANGES IN VERSION 1.0.8
------------------------

BUG FIXES

    o Trying to prevent R CMD BUILD from changing the behaviour of vignette
      code involving MotifDb package

CHANGES IN VERSION 1.0.7
------------------------

BUG FIXES

    o merge_motifs() will not show repeat families/organisms in new merged
      motif

    o show method will no longer show name slot instead of altname

CHANGES IN VERSION 1.0.6
------------------------

BUG FIXES

    o If MEME motif file has no strand info, assume `strand = "+"`, not
      `strand = c("+", "-")`

CHANGES IN VERSION 1.0.5
------------------------

BUG FIXES

    o `read_meme()` can now read non-DNA/RNA motifs

    o removed duplicate line in run_meme.R

    o `scan_sequences()` will not scan mismatching motif/sequence alphabets

    o verbose output from `scan_sequences()` will now display correctly

    o Using `enrich_motifs()` and not finding any motif hits in the input
      sequences no longer throws an error

    o Fixed threshold calculation in `enrich_motifs()`

    o `enrich_motifs()` will now show results for motifs which have hits in
      target sequences but none in bkg sequences

CHANGES IN VERSION 1.0.4
------------------------

BUG FIXES

    o Can now use `view_motifs(..., tryRC=F)` without throwing an error

CHANGES IN VERSION 1.0.3
------------------------

BUG FIXES

    o Missed a couple [Biostrings::*StringSet-class] from last patch

    o Updated README to reflect new installation method

    o Wrapped instances of \link{} with \code{\link{}}

CHANGES IN VERSION 1.0.2
------------------------

BUG FIXES

    o `read_meme()` can now read meme result files with missing strand info

    o Use \link{*StringSet} instead of [Biostrings::*StringSet-class] in
      documentation

    o No longer load MotifDb package in examples on Windows

CHANGES IN VERSION 1.0.1
------------------------

BUG FIXES

    o TFBSTools motifs with multiple species can convert to universalmotif

    o `scan_sequences()`: will now ignore non-standard letters instead of
      crashing

CHANGES IN VERSION 1.0.0
------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Changed the appearance of some of the vignette code blocks

    o More documentation added in data.R

BUG FIXES

    o Replaced for loop with `lapply()` in add_multifreq.R L120-133

    o Replaced for loop with `lapply()` in enrich_motifs.R L327-330

    o Replaced for loop with `lapply()` in shuffle_motifs.R L77-80

    o Using `diag()` instead of for loop in `fix_pcc_diag()` (compare_motifs.R)

    o Fixed `read_motifs()` not parsing alphabet correctly

    o Vignettes are now built using pdflatex instead of lualatex

CHANGES IN VERSION 0.99.0
-------------------------

    o Ready for bioconductor

CHANGES IN VERSION 0.98.0
-------------------------

    o Pre-bioconductor
