Updated to version 1.2.9 in the release and 1.3.9 in the development (23/08/2013) 23/08/2012 added consensusClustersTpm() function for retrieving matrix with tpm values for consensus clusters across all samples Updated to version 1.2.8 in the release and 1.3.8 in the development (23/08/2013) 22/08/2012 modified all functions to work on data from only one strand (some were previously giving error in such case) 21/08/2012 fixed the bug in calling CTSSs from reads on minus strand when not correcting for G addition, i.e. when removeFirstG=FALSE Updated to version 1.2.7 in the release and 1.3.7 in the development (08/08/2013) 08/08/2012 added new argument to aggregateTagClusters() function (excludeSignalBelowThreshold) that controls which TCs will contribute to the total CAGE signal of the consensus cluster - only the ones above the threshold that are used initially to set the boundaries of the consensus cluster, or all TCs that overlap the resulting consensus clusters 07/08/2012 enabled retrieving interquantile width for tag clusters - added new returnInterquantileWidth argument to tagClusters() function 06/07/2012 enabled importing entire CTSS table with multiple columns of tag counts representing multiple samples/experiments - allowed setting imputFilesType to "CTSStable" when creating CAGEset object and extended getCTSS function accordingly to read the entire table at once and fill the object Updated to version 1.2.6 in the release and 1.3.6 in the development (23/07/2013) 22/07/2012 replaced multicore package dependency with parallel package (suggested by Bioconductor core team) 21/07/2012 fixed the bug in using loaded genome when correcting for G nucleotide bias 20/07/2012 fixed plotReverseCumulatives to work with only one sample in the CAGEset 19/07/2012 changed naming of correlation plot files to distinguish CTSS from consensus clusters plot Updated to version 1.2.5 in the release and 1.3.5 in the development (28/06/2013) 28/06/2012 updated the vignette Updated to version 1.2.4 in the release and 1.3.4 in the development (16/06/2013) 16/06/2012 allowed plotting reverse cumulatives for normalized tag counts - added new argument to plotReverseCumulatives() function 15/06/2012 implemented calculating suggested referent power-law distribution and visualizing the distribution and its parameters on reverse cumulatives plot when calling plotReverseCumulatives() function 14/06/2012 allowed assigning user-specified colors to samples to be used in visualizations - added new setColors() function 13/06/2012 allowed plotting scatter plots and correlation for both individual TSSs (raw or normalized values) and consensus clusters - added new argument to plotCorrelation() function Updated to version 1.2.3. in the release and 1.3.3 in the development (12/06/2013) 12/06/2012 implemented plotting pairwise scatter plots of CAGE tag count and calculating correlation between samples - added new plotCorrelation() function Updated to version 1.2.2. in the release and 1.3.2 in the development (30/05/2013) 30/05/2013 implemented the algorithm for correcting 'G' nucleotide addition bias to CAGE tags described in Carninci et al., Nature Genetics 2006 - added a new option 'correctSystematicG' to getCTSS function Updated to version 1.2.1 in the release and 1.3.1 in the development (28/05/2013) 28/05/2013 fixed the bug in reporting number of CTSSs in cluster when clustering CTSSs using custom clusters (for empty clusters it was returning that the number of CTSSs is 1, although the signal is 0) 28/05/2013 fixed the bug in clustering CTSSs using custom clusters when run with multicore=FALSE (it was returning to many clusters - correct specified region but all of the regions on each chromosome, not only the specified one) 22/05/2013 fixed the column classes in CTSS data.frame when reading the data from bam files (to match the classes when reading from ctss files) 21/05/2013 updated the vignette with explanation on how to use custom build genomes 21/05/2013 allowed usage of custom build BSgenome packages by removing the check whether the specified genome is present in the available.genomes() from BSgenome package Updated to version 1.2.0 in the release and 1.3.0 in the development (02/05/2013) 02/05/2013 updated the vignette 02/05/2013 added a new feature in the plotReverseCumulatives function, so that the slope of the fitted power-law distribution in the user selected range of values is shown on the plot for each sample (helps to choose appropriate alpha parameter for normalization) 02/05/2013 fixed a bug in selecting the range of tag count values for fitting power-law distribution in normalization 01/05/2013 added sample labels as names to library sizes vector 29/04/2013 implemented statistical testing (Kolmogorov-Smirnov test) for differential promoter usage based on cumulative sums of CAGE signal along the promoters (implemented within the scoreShift function) 20/04/2013 added pass-through option "none" for 'method' parameter in normalizeTagCount function to enable using raw tag counts in downstream steps (CTSS clustering, promoter width, etc.) 19/04/2013 optimized scoreShift function to extract and process only the cumulative sums for samples being compared 19/04/2013 replaced lapply with a for loop in the scoreShift function to avoid invoking multicore within lapply 18/04/2013 fixed wrong error message in plotExpressionProfiles function that notifies about accepted values for 'what' parameter 27/03/2013 added data.table to the list of dependencies and optimized various parts of the code to use data.table instead of data.frame