Changes in version 0.99.13 o Fixed bugs that would cause ExCluster to either crash or not properly plot results in some cases Changes in version 0.99.12 o Loosened FDR calculations slightly (ExCluster was a bit too stringent) o Added plot.Type option to plotExonlog2FC function, which accepts "bitmap" and "PNG" o Bug-tested plot.Type so machines with at least Ghostscript or X11 forwarding will have minimal issues o Changed how files/folders are written & how write-permissions are detected, to avoid bugs o Updated the vignette to use BiocManager instead of biocLite Changes in version 0.99.11 o Removed some duplicated code (stripping ID numbers, computing p-values) o removed several instances of cat() and print() and replaced them with message() o changed apply() code to use matrixStats instead, which is up to 500 times faster (Thanks Lori!) o this previous change sped the algorithm up from 1 hour+ to only ~ 20 minute runtime o changed the test dataset so one of the genes has a p-value < 0.05 and plots results Changes in version 0.99.10 o The GFF_convert function now outputs GFF3 formatted annotations o Amended other functions (processCounts, ExCluster) to work on GFF3 formatted annotations o Changed the output of GFF_convert to be a GRanges object of said GFF3 annotations o Created a separate, internal, load_ExCluster_functions.R script to load helper functions o Removed many depenencies on variables outside the environment for said functions o Created a library of error messages in the ExCluster_errors.R script (internal) o Separated the large ExCluster function into ExCluster.R, ExClust_compute_stats.R, and ExClust_main_function.R Changes in version 0.99.9 o Added the function rtracklayerGTFtoGFF, which flattens GTF files imported by rtracklayer to GFF format o Added the function GRangesFromGFF, which converts GFF formatted data to GRanges format o Added the function GRangesFromExClustResults, which converts ExCluster function results to GRanges format o Removed repeated code from the GFF_convert function o Most functions now have checks to ensure GTF, GFF, and ExClustResults data is formatted correctly' o Made an improvement to the processCounts function, which handles some edge cases better (zero reads in some conditions) Changes in version 0.99.8 o Fixed build check errors from 0.99.7 Changes in version 0.99.7 o Fixed a number of bugs resulting from ExCluster() function code changes o Updated the Vignette to correctly reflect changes suggested from the Bioconductor review o Added several package imports to better keep track of global variables/functions o Reduced the lengths of code lines in a number of instances o Cleaned up error messages for ExCluster() function Changes in version 0.99.6 o Completely re-wrote the GFF_convert() function to have helper functions and take advantage of GenomicRanges o Changed processCounts, which was incorrectly counting reads as stranded (is now set to unstranded) o Altered ExCluster null hypothesis simulations to run faster (about 4 times faster now) o Made numerous small changes to address the issues with first Bioconductor review Changes in version 0.99.5 o Fixed incorrectly pushed changes, which caused build error Changes in version 0.99.4 o Reformatted the Vignette & DESCRIPTION to process the Vignette correctly with Sweave Changes in version 0.99.3 o Removed extraneous files causing errors in the build Changes in version 0.99.2 o Reformatted the Vignette & DESCRIPTION to process the Vignette correctly with Sweave Changes in version 0.99.1 o Removed extraneous files causing errors in the build Changes in version 0.99.0 o ExCluster package now passes R CMD build and check, and BiocCheck! o takes about 2-3 hours to run on large datasets o added a "Toy Dataset" for function manual runnable examples within the package o more code in ExCluster has been turned into functions to reduce repeated code o still some repeated code (such as parsing EnsIDs and exon bins)