0.1.0 (01-09-2017) + Code has been tested and is stable. Preparing for submission to Bioconductor once vignette (and various other requirements) is complete. 0.2.0 (01-18-2017) + Vignette completed testing 0.99.0 (01-20-2017) + Package (version 0.99.0) submitted to Bioconductor for review 0.99.2 (02-24-2017) + Revised package (version 0.99.2) submitted to Bioconductor for further review 0.99.2 (04-18-2017) + Revised package (version 0.99.2) submitted to Bioconductor for review 1.0.0 (04-19-2017) + Package accepted (version 1.0.0) at Bioconductor, included in version 3.5. 1.2.0 (09-26-2017) + Support added for the analysis of ESTs/cDNAs; BED files can now be provided as input (version 1.2.0) 1.2.1 (10-17-2017) + Minor changes in documentation to better reflect updates in v. 1.2 (version 1.2.1). 1.8.0 (07-10-2018) + Additional promoter (TSR) metrics added to output, including the modified shape index (mSI) and torque. + Modifications to column IDs to reflect updated nomenclature. + Updates to User's Guide in addition to creation of Singularity recipe for reproucible analysis across platforms. 1.8.9 (10-08-2018) + Updates that correct a speed issue encountered when analyzing data aligned to assemblies with many scaffolds. + Simplified part of one vignette. 1.10.12 (09-17-2019) + Updates to include 3'-read capturing from bam input files and data structures to allow ignoring spurious TSSs. + Added capabilities for sorting by strand (and seq/TSS) for TSS merging. + Made a change leading to a substantial speed-up of mergeSampleData(). + Added qname to saved columns from .bam input. + Minor changes to writeTSR() and writeTSS(). + Rewrite to mergeSampleData). + Improvements to loadTSSobj(). + Necessary updates to the Singularity recipe to reflect the above changes. 1.12.1 (10-31-2019) + Version bump due to release of Bioconductor v. 3.10. 1.12.2 (11-01-2019) + Corrected minor bug in non-user-level function detTSR() 1.12.3 (11-21-2019) + added support for BedGraph format in both writeTSS() and writeTSR() + updated documentation for loadTSSobj() for the sake of clarity. 1.12.4. (12-16-2019) + Added feature to writeTSS() that generates two separate bedgraph files (plus and minus) instead of one.