Changes in version 1.9 o Fixed bug in the bootstrap method for bumphunter. The coefficient for which inference was calculated was always 2 instead of the coefficient coef passed as an argument. Changes in version 1.3 o Fixed NAMESPACE issues. o nearestgene() now loads TT.rda into the local environment o known_transcripts(), and consequently matchGenes(), was yielding mostly NA for the Refseq / 'annotation' column (iff there were multiple refseq ids for the given Entrez/Gene id) o Fixed data/TT.rda, as the new value of known_transcripts(). o Cleaned up NEWS. o Added GitHub URL to DESCRIPTION. o Cleaned up duplicates in Suggests:. Changes in version 1.1 o Added NEWS file. o Fixed a bug related to >= for numerics. o Added smoothing using a gaussian kernal as implemented in the locfit package through the function locfitByCluster. o Added closeSockets for cleanup for doParallel on Windows. o More bugfixes for windows; now using foreachCleanup(). o Added a 'bumps' class and print method. o annotateNearest / regionMatch now give NA annotations for queries with no nearest subject (perhaps because the seqname is missing from the subject). Previously this was taken to be mistaken input and a hard error raised. o Speedup of fwer computations using foreach. o Added boundedClusterMaker. o bug fix to internal function .getModT (which are not used in the main bumphunter functions). Now the t-statistics returned a correct.