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